Patent Application
20140113830
The present invention relates to an azoline compound library, an azole compound library, and the like.
In recent years, a variety of peptides has attracted attentions as a drug candidate or research tool. There have been various attempts to develop a peptide library and screen peptides having affinity with a target substance.
As a method of artificially constructing a peptide library, a method using chemical synthesis, a method using a biosynthetic enzyme of a secondary metabolite, and a translation synthesis system, and the like have been employed conventionally.
It is however difficult, in the method using chemical synthesis, to increase the diversity of a library. In addition, it takes time for screening or analyzing the relationship between the structure of a compound and activity.
The method of using a biosynthetic enzyme of a secondary metabolite, on the other hand, enables rapid and easy construction or chemical conversion of a precise backbone that is difficult to be achieved by the chemical synthesis method. Since enzymes have substrate specificity, however, kinds of compounds that can be synthesized are limited. This method is therefore not suited for use in the construction of a compound library with highly diverse kinds of molecules.
When a translation system is used, a peptide library rich in diversity can be constructed in a short time by constructing an mRNA library and translating it in one pot. By using this system in combination with an mRNA display method or the like, both a peptide selected by screening and information on a nucleic acid encoding such peptide can be obtained simultaneously so that the genotype and the phenotype of the selected peptide can be related to each other easily. Despite the fact that synthesis of a peptide library using such a translation system has many advantages, it can only produce compounds consisting of peptidic backbone.
In screening using a library, identification of a compound inhibiting a target substance having protease activity is often required. The library of peptidic compounds is however cleaved by protease, and thus compounds inhibiting the activity of a target substance cannot be screened efficiently.
Each peptide of the peptide library may be modified in vitro with a post-translational modification enzyme, but an enzyme having a desired activity does not always have activity in vitro. In addition, the expressed peptide library should be purified prior to the reaction with an enzyme, and investigation of substrate specificity of the enzyme is also required. It is therefore not easy to obtain a library comprised of peptides having a desired structure.
A library in which the presence or absence, or degree of modification of each member cannot be identified is inferior in usefulness because it eventually requires correlation analysis between structure and activity, as in the chemical synthesis system.
Patellamide produced by Prochloron didemni, that is, endozoic algae of sea squirt is a low molecular cyclic peptide which is presumed to have various physiological activities and it is biosynthesized via a unique pathway with products of a pat gene cluster consisting of patA to patG. The pat gene cluster and biosynthesis pathway of patellamide are schematically shown in
In this biosynthesis, PatE peptide which is a patE gene product serves as a precursor. Since the patE gene has a hypervariable region (cassette domain), the product of it constructs a natural combinatorial library.
The PatE peptide has, on both sides of the cassette domain, a recognition sequence by a post-translational modification enzyme. PatA, PatD, and PatG serve as the post-translational modification enzyme. Pat D introduces an azoline backbone into Cys, Ser, and Thr in the cassette of PatE and converts Cys to a thiazoline backbone and Ser and Thr into an oxazoline backbone.
PatE cleaves the recognition sequence at the N-terminus side of the cassette domain of the PatE.
PatG is composed of two domains. An oxidase domain on the N-terminus side converts an azoline backbone introduced by PatD into an azole backbone, that is, converts a thiazoline backbone into an azole backbone. A peptidase domain on the C-terminus side macrocyclizes PatE, while cleaving the recognition sequence on the C-terminus side of the cassette domain of PatE.
With regard to the cassette domain of the above-mentioned natural PatE, sequences shown in the following table are described in M. S. Donia et al. (Non-patent Document 1).
ulithiacyclamide
lissoclinamide 2/3
These tables show that sequences of natural cassette domains have following similarities: (i) they have 7 or 8 residues, (ii) they tend to have Ser/Thr/Cys to be modified at 2, 4, 6, or 8 positions from the N-terminus of the cassette domain, (iii) the residues (Ser, Thr, and Cys) to be modified are not adjacent to each other in most cases, and (iv) many of the residues other than Ser, Thr, and Cys are hydrophobic residues such as Val, Ala, Ile, Phe, and Leu.
These similarities were presumed to be necessary for becoming a substrate of PatD or PatG, a post-translational modification enzyme. It is however not known which residue of Ser, Thr, and Cys has been modified or not modified and substrate specificity of PatD and PatG has not been elucidated yet.
An object of the present invention is to provide a method of efficiently constructing a library having sufficient diversity and usable for screening of a compound that binds to a target substance even having protease activity.
The present inventors considered that a library usable for screening of compounds that bind to a target substance having protease activity can be obtained and the above-mentioned problem can be solved if a PatE library more abundant in diversity than natural one can be obtained efficiently by some method and if modification with a post-translational modification enzyme can be made by using such library as a substrate.
As a result of further investigation described herein, we found that some of azoline backbone-introducing enzymes have azoline backbone forming activity even in vitro; and the sequence of the cassette domain which is a substrate of such an azoline backbone-introducing enzyme is not limited to that described in M. S. Donia et al. but a cassette domain having from 2 to 40 amino acid residues may also be a substrate of the enzyme and Cys, Ser, Thr, and 2,3-diamino acid and analogs thereof in the cassette domain can be converted into an azoline backbone.
It has further been confirmed that steps of expressing a PatE library in a cell-free translation system by using a precursor peptide comprising, in the order of mention from the N-terminus, a leader sequence of PatE, a recognition sequence 1 by an azoline backbone-introducing enzyme, a cassette domain, and a recognition sequence 2 by the azoline backbone-introducing enzyme, modifying it with the azoline backbone-introducing enzyme, and cutting off an unnecessary region can be conducted efficiently in one pot and as a result, an azoline compound library sufficiently abundant in diversity and usable for screening using even a target substance having protease activity can be obtained.
We also found that the above-mentioned precursor peptide may be a substrate of an azoline backbone-introducing enzyme when, in the above-mentioned precursor peptide, only a portion of a conventionally known leader sequence is used as the leader sequence of PatE or the leader sequence is completely removed; when sequences different from those conventionally known as the recognition sequence 1 or 2 is used; when the recognition sequences 1 and 2 are removed; or the like. Moreover, it has been confirmed that even if as the leader sequence portion, a peptide separated from a precursor peptide comprising a cassette domain is used, as long as the peptide is present in a reaction system, the precursor peptide comprising a cassette domain may be a substrate of an azoline backbone-introducing enzyme, leading to the completion of the present invention.
The present invention relates to:
A-(Xaa0)m-B (I)
(wherein, m numbers of Xaa0s respectively represent arbitrary amino acids, at least one of which is an amino acid selected from the group consisting of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof, m represents an integer selected from 2 to 40, and A and B each independently represent a peptide composed of from 0 to 100 amino acids), including:
a step of constructing an mRNA library encoding a precursor peptide comprising, in order of mention from the N-terminus, a recognition sequence 1 by an azoline backbone-introducing enzyme, -(Xaa0)m-, and a recognition sequence 2 by the azoline backbone-introducing enzyme (the recognition sequences 1 and 2 being recognition sequences by the azoline backbone-introducing enzyme each composed of from 0 to 10 amino acids);
a step of expressing the precursor peptide in a cell-free translation system by using the mRNA library and thereby constructing a peptide library; and
a step of reacting the azoline backbone-introducing enzyme and the peptide library in the presence of a peptide comprising a leader sequence of a substrate of the azoline backbone-introducing enzyme and thereby introducing an azoline backbone into at least one of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof of Xaa0 (the leader sequence being a leader sequence of a substrate of the azoline backbone-introducing enzyme composed of from 0 to 50 amino acid);
[2] a method of constructing an azoline compound library containing two or more complexes between an azoline compound having an azoline backbone introduced into at least one of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof of Xaa0 of a peptide represented by the following formula (I):
A-(Xaa0)m-B (I)
(wherein, m numbers of Xaa0s respectively represent arbitrary amino acids, at least one of which represents an amino acid selected from the group consisting of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof, m represents an integer selected from 2 to 40, and A and B each independently represent a peptide composed of from 0 to 100 amino acids) and an mRNA encoding the peptide represented by the formula (I), including:
a step of constructing an mRNA library encoding a precursor peptide comprising, in order of mention from the N-terminus, a recognition sequence 1 by an azoline backbone-introducing enzyme, -(Xaa0)m-, and a recognition sequence 2 by the azoline backbone-introducing enzyme (the recognition sequences 1 and 2 being recognition sequences by the azoline backbone-introducing enzyme each composed of from 0 to 10 amino acids);
a step of binding a puromycin to the 3′ end of each mRNA of the mRNA library to construct a puromycin bound mRNA library;
expressing the precursor peptide in a cell-free translation system by using the puromycin-bound mRNA library and constructing a peptide-mRNA complex library; and
a step of reacting the azoline backbone-introducing enzyme and the peptide-mRNA complex library in the presence of a peptide comprising a leader sequence of a substrate of the azoline backbone-introducing enzyme and introducing an azoline backbone into at least one of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof of Xaa0 (the leader sequence being a leader sequence of a substrate of the azoline backbone-introducing enzyme composed of from 0 to 50 amino acid);
[3] the method of constructing an azoline compound library as described above in [1] or [2], wherein:
in the formula (I), -(Xaa0)m- means -(Xaa1-Xaa2)n- (wherein, n numbers of Xaa1 each independently represent an arbitrary amino acid, n numbers of Xaa2 each independently represent an amino acid selected from the group consisting of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof, and n represents an integer selected from 1 to 20); and
an azoline backbone has been introduced into at least one of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof of Xaa1 and Xaa2 of the azoline compound;
[4] the method as described above in any one of [1] to [3], wherein at least one of the peptides represented by the formula (I) is a peptide having at least one of the following characteristics (i) to (iv):
(i) m represents from 2 to 40 (with the proviso that 7 and 8 are excluded);
(ii) n represents from 1 to 20 (with the proviso that 3 and 4 are excluded);
(iii) at least one of Xaa1s is an amino acid selected from Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof; and
(iv) at least one of Xaa1s is a hydrophilic amino acid;
[5] the method as described above in any one of [1] to [3], wherein at least one of the peptides represented by the formula -(Xaa0)m- is a peptide represented by any of SEQ ID NOS: 10 to 57;
[6] the method as described above in any one of [1] to [5], wherein at least one of the azoline compounds has 5 or more azoline backbones;
[7] the method as described above in any one of [1] to [6], wherein each of the mRNAs of the mRNA library is constituted so that each peptide comprising the leader sequence is expressed as a fusion peptide with the precursor peptide comprising a recognition sequence 1, -(Xaa0)m-, and a recognition sequence 2;
[8] the method as described above in [7], further comprising, after introduction of the azoline backbone, a step of cleaving the leader sequence from the precursor peptide;
[9] the method as described above in any one of [1] to [6], wherein in the step of introducing an azoline backbone, the peptide comprising a leader sequence is separated from the precursor peptide comprising a recognition sequence 1, -(Xaa0)m-, and a recognition sequence 2;
[10] the method as described above in any one of [1] to [9], further comprising a step of macrocyclizing the azoline compound;
[11] the method of constructing an azole compound library, comprising, after the step of introducing an azoline backbone in the method of constructing an azoline compound library according to any one of claims 1 to 10, a step of reacting the library having an azoline backbone introduced therein with an azole backbone-introducing enzyme in the presence or absence of a peptide comprising a leader sequence of a substrate of the azole backbone-introducing enzyme and converting at least one of the azoline backbones into an azole backbone (the leader sequence meaning a leader sequence of a substrate of the azoline backbone-introducing enzyme composed of from 0 to 50 amino acids);
[12] the method as described above in [11], wherein the azole backbone-introducing enzyme is a mutant of PatG that has lost the peptidase domain thereof or that has lost the peptidase activity by point mutation;
[13] an azoline compound library containing two or more azoline compounds having an azoline backbone introduced into at least one of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof of Xaa0 of a peptide represented by the following formula (I):
A-(Xaa0)m-B (I)
(wherein, m numbers of Xaa0s respectively represent arbitrary amino acids, at least one of which is an amino acid selected from the group consisting of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof, m represents an integer selected from 2 to 40, and A and B each independently represent a peptide composed of from 0 to 100 amino acids), wherein:
in at least one of the peptides represented by the formula (I), m does not represent 7 or 8;
[14] the azoline compound library as described above in [13], wherein in the formula (I), -(Xaa0)m- means -(Xaa1-Xaa2)n- [wherein, n numbers of Xaa1 each independently represent an arbitrary amino acid, n numbers of Xaa2 each independently represent an amino acid selected from the group consisting of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof, and n represents an integer selected from 1 to 10]; and
at least one of the peptides represented by the formula (I) is a peptide having at least one of the following characteristics (i) to (iv):
(i) m represents from 2 to 40 (with the proviso that 7 and 8 are excluded);
(ii) n represents from 1 to 20 (with the proviso that 3 and 4 are excluded);
(iii) at least one of Xaa1s is an amino acid selected from Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof; and
(iv) at least one of Xaa1s is a hydrophilic amino acid;
[15] the azoline compound library as described above in [13] or [14], wherein each of the azoline compounds forms a complex with an mRNA encoding the peptide portion of the azoline compound;
[16] the azoline compound library as described above in any one of [13] to [15], wherein the entirety or a portion of the recognition sequence by the azoline backbone-introducing enzyme has been bound to the N-terminus and C-terminus of the peptide represented by the formula (I);
[17] an azole compound library containing two or more azole compounds having an azole backbone introduced into at least one of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof of Xaa0 of a peptide represented by the following formula (I):
A-(Xaa0)m-B (I)
[wherein, m numbers of Xaa0s represent arbitrary amino acids, at least one of which is an amino acid selected from the group consisting of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof, m represents an integer selected from 2 to 40, and A and B each independently represents a peptide composed of from 0 to 100 amino acids], wherein:
in at least one of the peptides represented by the formula (I), m does not represent 7 or 8;
[18] the azole compound library as described above in [17], wherein in the formula (I), -(Xaa0)m- means -(Xaa1-Xaa2)n- [wherein, n numbers of Xaa1 each independently represent an arbitrary amino acid, n numbers of Xaa2 each independently represent an amino acid selected from the group consisting of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof, and n represents an integer selected from 1 to 20); and
at least one of the peptides represented by the formula (I) has at least one of the following characteristics (i) to (iv):
(i) m represents from 2 to 40 (with the proviso that 7 and 8 are excluded);
(ii) n represents from 1 to 20 (with the proviso that 3 and 4 are excluded);
(iii) at least one of Xaa1s is an amino acid selected from Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof; and
(iv) at least one of Xaa1s is a hydrophilic amino acid;
[19] the azole compound library as described above in [17] or [18], wherein each of the azole compounds forms a complex with an mRNA encoding the peptide portion of the compound;
[20] the azole compound library as described above in any one of [17] to [19], wherein the entirety or a portion of the recognition sequence by the azoline backbone-introducing enzyme binds to the N-terminus and C-terminus of the peptide represented by the formula (I);
[21] a screening method for identifying an azoline compound that binds to a target substance, including:
a step of bringing the azoline compound library constructed by using any one of the methods described in from [1] to [10] or the azoline compound library as described above in any one of [13] to [16] into contact with a target substance, followed by incubation, and a step of selecting the azoline compound that has bound to the target substance;
[22] a screening method for identifying an azoline compound that binds to a target substance, including:
a step of bringing the azoline compound library constructed by using any one of the methods described in from [2] to [10] or the azoline compound library as described above in [15] or [16] into contact with a target substance, followed by incubation,
a step of selecting an azoline compound that has bound to the target substance, and
a step of analyzing the base sequence of the mRNA of the thus-selected azoline compound;
[23] a screening method for identifying an azole compound that binds to a target substance, including:
a step of bringing the azole compound library constructed by using the method described in [11] or [12] or the azole compound library as described above in any one of from [17] to [20] into contact with a target substance, followed by incubation, and
a step of selecting an azole compound that has bound to the target substance;
[24] a screening method for identifying an azole compound that binds to a target substance, including:
a step of bringing the azole compound library constructed by using the method described in [11] or [12] or the azole compound library as described above in [19] or [20] into contact with a target substance, followed by incubation,
a step of selecting an azole compound that has bound to the target substance, and
a step of analyzing the base sequence of the mRNA of the thus-selected azole compound;
[25] a screening kit for identifying an azoline compound that binds to a target substance, including:
the azoline compound library constructed by using the method as described in any one of from [1] to [10] or the azoline compound library as described above in any one of from [13] to [16];
[26] the kit as described above in [25], wherein the library has been immobilized onto a solid phase support;
[27] a screening kit for identifying an azole compound that binds to a target substance, including:
the azole compound library constructed by using the method as described above in [11] or [12] or the azole compound library as described above in any one of from [17] to [20];
[28] the kit as described above in [27], wherein the library has been immobilized onto a solid phase support;
[29] a method of preparing an azoline compound having an azoline compound introduced into at least one of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof of Xaa0 of a peptide represented by the following formula (I):
A-(Xaa0)m-B (I)
[wherein, m numbers of Xaa0s represent arbitrary amino acids, at least one of which is an amino acid selected from the group consisting of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof, m represents an integer selected from 2 to 40, and A and B each independently represent a peptide composed of from 0 to 100 amino acids), including:
a step of preparing an mRNA encoding a precursor peptide comprising, in order of mention from the N-terminus, a recognition sequence 1 by an azoline backbone-introducing enzyme, -(Xaa0)m-, and a recognition sequence 2 by the azoline backbone-introducing enzyme (the recognition sequences 1 and 2 being recognition sequences by the azoline backbone-introducing enzyme each composed of from 0 to 10 amino acids);
a step of expressing the precursor peptide in a cell-free translation system by using the mRNA; and
a step of reacting the azoline backbone-introducing enzyme and the precursor peptide in the presence of a peptide comprising a leader sequence of a substrate of the azoline backbone-introducing enzyme and thereby introducing an azoline backbone into at least one of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof of Xaa0 (with the proviso that the peptide comprising the leader sequence is separated from the precursor peptide comprising the recognition sequence 1, -(Xaa0)m-, and the recognition sequence 2);
[30] a method of preparing an azole compound including:
a step of reacting the azoline compound prepared by using the method as described above in [29] and an azole backbone-introducing enzyme in the presence or absence of a peptide comprising a leader sequence of a substrate of the azole backbone-introducing enzyme and thereby converting at least one of the azoline backbones into an azole backbone; and
[31] a kit for preparing an azoline compound or an azole compound, comprising an azoline backbone-introducing enzyme or azole backbone-introducing enzyme and a peptide comprising a leader sequence of a substrate of the azoline backbone-introducing enzyme.
The method of the present invention makes it possible to rapidly and easily provide an azoline compound library and an azole compound library much more abundant in diversity than a natural PatE library.
By using such an azoline compound or azole compound library, an azoline compound or azole compound that binds to a target substance having protease activity can be screened.
In addition, when an mRNA display method is applied to the azoline compound or azole compound library of the present invention and a library of complexes between an azoline compound or azole compound and an mRNA encoding the peptide portion thereof is constructed, it is possible to determine a nucleic acid sequence encoding the azoline compound/azole compound identified by screening and thereby easily analyze the relationship between the structure and activity of the compound.
The present invention provides a construction method of an azoline compound library including two or more azoline compounds.
The term “azoline compound” as used herein means a compound having an azoline backbone introduced into at least one of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof of a peptide represented by the following formula (I):
A-(Xaa0)m-B (I)
[wherein, m numbers of Xaa0s represent arbitrary amino acids, at least one of which represents an amino acid selected from the group consisting of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof, m represents an integer selected from 2 to 40, and A and B each independently represent a peptide composed of from 0 to 100 amino acids].
In one embodiment of the present invention, the azoline compound is represented by the formula (I) in which -(Xaa0)m- is -(Xaa1-Xaa2)n- [wherein, n numbers of Xaa1s each independently represent an arbitrary amino acid, n numbers of Xaa2s each independently represent an amino acid selected from the group consisting of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof, and n represents an integer selected from 1 to 20].
The Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof into which the azoline backbone has been introduced may be either at a position of Xaa1 or at a position of Xaa2.
The term “amino acid” is used herein in the broadest meaning and includes, in addition to natural amino acids, artificial amino acid mutants and derivatives. Examples of the amino acid as described herein include natural proteinogenic L-amino acids; D-amino acids; chemically modified amino acids such as amino acid mutants and derivatives; natural non-proteinogenic amino acids such as norleucine, β-alanine, and ornithine; and chemically synthesized compounds having properties known per se in the art and characteristic to amino acids. Examples of the non-natural amino acids include α-methylamino acids α-methylalanine, etc.), D-amino acid, histidine-like amino acids (β-hydroxy-histidine, homohistidine, α-fluoromethyl-histidine, α-methyl-histidine, etc.), amino acids (“homo” amino acids) having, on the side chain thereof, extra methylene, and amino acids (cysteic acid, etc.) obtained by substituting, with a sulfonic acid group, a side-chain amino acid with a carboxylic acid functional group.
The amino acid herein is represented by commonly used single-letter or three-letter code. The amino acids represented by single-letter or three-letter code include mutants and derivatives thereof.
Examples of the analogs of Thr include, but not limited to those represented by the following formula:
[wherein, R represents a hydrogen atom, a substituted or unsubstituted alkyl group having from 1 to 10 carbon atoms, or a substituted or unsubstituted aromatic group].
Examples of the analogs of Cys include, but not limited to, those represented by the following formula:
[wherein, R represents a hydrogen atom, a substituted or unsubstituted alkyl group having from 1 to 10 carbon atoms, or a substituted or unsubstituted aromatic group].
Examples of the analogs of Ser or Thr include, but not limited to, those represented by the following formulas:
Examples of the 2,3-diamino acid and analogs thereof include, but not limited to, those represented by the following formulas:
[wherein, R represents a hydrogen atom, a substituted or unsubstituted alkyl group having from 1 to 10 carbon atoms, or a substituted or unsubstituted aromatic group].
The term “introducing an azoline backbone into at least one of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof” as used herein means that a dehydration reaction occurs at Cys, Ser, Thr, or 2,3-diamino acid to introduce an azoline ring represented by the following formulas:
Introduction of an azoline backbone into Ser, Thr, Cys, or 2,3-diaminopropionic acid produces an oxazoline, thiazoline backbone, or an imidazoline backbone as follows:
For example, introduction of an azoline backbone into the above-mentioned Thr analogue residue produces the following oxazoline backbone.
Introduction of an azoline backbone into the above-mentioned Cys analog residue produces the following imidazoline backbone.
Introduction of an azoline backbone into the above-mentioned 2,3-diamino acid analog residue produces the following thiazoline backbone.
In the above formula (I), Xaa0 represents an arbitrary amino acid insofar as it contains at least one of Cys, Ser, Thr, 2,3-diamino acid, and an analog thereof. As described above, although it has been considered that an azoline backbone-introducing enzyme such as PatD modifies only a cassette domain having 7 or 8 amino acids and having predetermined regularity, a wide sequence with m of from 2 to 40 becomes a substrate.
In the above-mentioned formula (I), Xaa1s each independently represent an arbitrary amino acid. As described above, it has been conventionally considered that in peptide which is a substrate of an azoline backbone-introducing enzyme such as PatD, residues to be modified rarely be adjacent to each other, but as shown in Examples which will be described later, even if Xaa1 represents Cys, Ser, or Thr and is the same amino acid as that of Xaa2 adjacent thereto, the peptide of the formula (I) may be a substrate of an azoline backbone-introducing enzyme.
In addition, it has been conventionally considered that in peptide which may be a substrate of an azoline backbone-introducing enzyme such as PatD, many of residues other than Ser, Cys, and Thr are hydrophobic amino acid residues, but as shown later in Examples, a peptide having, as Xaa1 thereof, a hydrophilic amino acid may be a substrate of an azoline backbone-introducing enzyme.
In the above formula (I), m represents an integer of 2 or greater, and 16 or less, 18 or less, 20 or less, 30 or less, or 40 or less; and n represents an integer of 1 or greater, and 8 or less, 9 or less, 10 or less, or 20 or less. As described above, it has conventionally been considered that in the peptide which may be a substrate of an azoline backbone-introducing enzyme such as PatD, m=7 or 8, meaning that n=3 or 4, but as will be shown later by Examples, the peptide of the formula (I) having, as m, 9 or greater and, as n, 5 or greater may also be a substrate of the azoline backbone-introducing enzyme.
In the above formula (I), A and B each independently represent a peptide composed of from 0 to 100 amino acids. A may contain the entirety or a portion of a recognition sequence 1 of an azoline backbone-introducing enzyme. It may contain the entirety or a portion of a leader sequence of PatE, a His tag, a linker, and the like. B may contain the entirety or a portion of a recognition sequence 2. It may contain a His tag, a linker, and the like. A and B each may have a length of, for example, 100, 70, 60, 50, 40, 30, 20, 10, 5, 2, 0 amino acid(s), but the length is not limited thereto. In A or B, one or several amino acids may be a modified amino acid or amino acid analog.
The construction method of an azoline compound library according to one embodiment of the present invention includes a step of constructing an mRNA library encoding a precursor peptide comprising, in order of mention from the N-terminus, the recognition sequence 1 of an azoline backbone-introducing enzyme, the (Xaa1-Xaa2)n-, and the recognition sequence 2 of an azoline backbone-introducing enzyme.
The recognition sequences 1 and 2 of an azoline backbone-introducing enzyme are recognition sequences composed of from 0 to 10 amino acids and to be recognized by an azoline backbone-introducing enzyme. They may have any sequence insofar as the azoline backbone-introducing enzyme recognizes them and introduce an azoline backbone into -(Xaa0)m-. When the azoline backbone-introducing enzyme is PatD, for example, G(A/L/V) (G/E/D) (A/P) (S/T/C) (SEQ. ID NO: 2) can be used as the recognition sequence 1. It may be, for example, GLEAS (SEQ. ID NO: 3). As the recognition sequence 2 by the azoline backbone-introducing enzyme, that containing (A/S)Y(D/E)G(A/L/V) (SEQ ID NO:4) can be used. As such a sequence, for example, AYDGVEPS (SEQ ID NO: 5), AYDGV (SEQ ID NO: 6), AYDGVGSGSGS (SEQ ID NO: 7), AYDGVGGGGGG (SEQ ID NO: 8), or AYDGVEGSGSGS (SEQ ID NO: 9) may be used.
As shown later in Examples, the above-mentioned precursor peptide may become a substrate of the azoline backbone-introducing enzyme even if it does not have the recognition sequence 1 and/or 2, and thus the recognition sequences 1 and 2 are optional constituting elements of the precursor peptide.
Further, as shown later in Examples, the above-mentioned precursor peptide may become a substrate of the azoline backbone-introducing enzyme even if it uses a sequence utterly unrelated to sequences conventionally known as a recognition sequence.
In particular, the precursor peptide having the recognition sequence 1 on the N-terminus side of -(Xaa1-Xaa2)n- is susceptible to modification with the azoline backbone-introducing enzyme but the sequence is not particularly limited insofar as it is present. As the recognition sequence 1, a sequence, for example, GGGGG, QQQQQ, LLLLL, or PPPPP may be used.
As will be described later, the above-mentioned precursor peptide may be fused further with a peptide having, on the N-terminus side thereof, a leader sequence.
The leader sequence, the recognition sequence 1 by the azoline ring-introducing enzyme, -(Xaa0)m-, and the recognition sequence 2 by the azoline ring-introducing enzyme may be adjacent to each other in the precursor peptide. The precursor peptide may have a sequence of from one to several amino acids between the leader sequence, the recognition sequence 1, -(Xaa0)m-, and the recognition sequence 2 insofar as it is expressed as a precursor peptide in a cell-free expression system and is subjected to modification with the azoline ring-introducing enzyme.
An mRNA library encoding -(Xaa0)m- can be constructed by synthesizing a DNA containing a sequence such as -(NNN)n-, -(NNK)n-, -(NNU)n-, or —(NNG)n- and transcribing it. Here, the “N” means any one of A, C, G, and T; “K” means either one of G and T; NNN and NNK each mean any one of 20 protein amino acids; and NNU and NNG encode any one of 15 and 14 protein amino acids, respectively.
An mRNA library encoding -(Xaa1-Xaa2)n- can be constructed, for example, by synthesizing a DNA containing a sequence such as —(NNK-WSU)n- or —(NNK-UGU)n- and transcribing it. Here, N means any one of A, C, G, and T; K means either one of G and T; W means either one of A and T; and S means either one of C and G. NNN and NNK each encode any one of 20 protein amino acids; WSU encodes any one of Ser, Thr, and Cys; and UGU encodes Cys.
When such a constitution is employed, a sufficient size of library can be obtained. For example, in the case of -(Xaa0)m- and m=10, 2010 kinds of variants can be prepared theoretically even from only 20 natural amino acids; and in the case of -(Xaa1-Xaa2)n- and n=5, 205×35 kinds of mutants can be prepared.
By synthesizing a DNA encoding -(Xaa0)m-, containing, at the 5′ end thereof, a DNA encoding the recognition sequence 1 and, at the 3′ end thereof, a DNA encoding the recognition sequence 2 and transcribing it, an mRNA encoding a precursor peptide comprising the recognition sequence 1, -(Xaa1-Xaa2)n-, and the recognition sequence 2 can be obtained. By synthesizing a DNA further containing, on the 5′ end side of the DNA encoding the recognition sequence 1, a DNA encoding a leader sequence and transcribing it, an mRNA encoding a precursor peptide comprising the leader sequence, the recognition sequence 1, -(Xaa1-Xaa2)n-, and the recognition sequence 2 can be obtained.
The construction method of an azoline compound library according to one embodiment of the present invention includes a step of using the above-mentioned mRNA library to express the above-mentioned precursor peptide with a cell-free translation system and thereby constructing a peptide library.
The cell-free translation system contains, for example, ribosome protein, aminoacyl tRNA synthetase (ARS), ribosome RNA, amino acid, GTP, ATP, translation initiation factor (IF), extension factor (EF), release factor (RF), ribosome regeneration factor (RRF), and other factors necessary for translation. An Escherichia coli extract or wheat germ extract may be used for enhancing the expression efficiency. Alternatively, a rabbit erythrocyte extract or insect cell extract may be used.
From several hundred micrograms to several milligram/mL of proteins can be produced by continuously supplying the system containing them with energy under dialysis. The system may contain an RNA polymerase for simultaneously conducting transcription from a gene DNA. Commercially available cell-free translation systems that can be used include E. coli-derived systems such as “RTS-100” (registered trademark), product of Roche Diagnostics and “PURESYSTEM” (registered trademark), product of PGI and systems using a wheat germ extract available from ZOEGENE Corporation and CellFree Sciences Co., Ltd.
When the cell-free translation system is used, a peptide can be modified in one pot by adding a post-translation modification enzyme to the same container without purifying an expression product.
The construction method of an azoline compound library according to one embodiment of the present invention includes a step of reacting an azoline backbone-introducing enzyme and the above-mentioned peptide library in the presence of a peptide comprising a leader sequence of a substrate of the azoline backbone-introducing enzyme, and thereby introducing an azoline backbone into at least one of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof. More specifically, an oxazoline backbone is introduced into Ser and Thr, a thiazoline backbone is introduced into Cys, and an imidazoline backbone is introduced into 2,3-diamino acid.
The leader sequence is a sequence that facilitates modification with the azoline backbone-introducing enzyme and any sequence may be used insofar as it satisfies this object. As will be described later in Examples, the precursor peptide comprising the recognition sequence 1, -(Xaa1-Xaa2)n-, and the recognition sequence 2 may become a substrate of the azoline backbone-introducing enzyme without the leader sequence. The leader sequence may be composed of, for example, about 5 amino acids, about 7 amino acids, about 10 amino acids, about 20 amino acids, about 30 amino acids, about 40 amino acids, or about 50 amino acids.
As the leader sequence, for example, a peptide composed of the following amino acid sequence; a partial sequence of this amino acid sequence; or an amino acid sequence obtained by deleting, adding, or substituting one to several amino acids in this amino acid sequence may be used.
MNKKNILPQQGQPVIRLTAGQLSSQLAELSEEALGDA (SEQ ID NO: 1)
The partial sequence of the amino acid sequence having SEQ ID NO: 1 is a sequence containing at least four successive amino acids, five successive amino acids, or six successive amino acids of this amino acid sequence. Although no particular limitation is imposed on the position of these amino acids in SEQ ID No: 1, the partial sequence contains four amino acids, five amino acids, or six amino acids, for example, at the C-terminus of the amino acid sequence of SEQ ID NO: 1.
Further, as will be shown later in Examples, the above-mentioned precursor peptide may become a substrate of an azoline backbone-introducing enzyme even when using, as the leader sequence, a sequence entirely unrelated to a leader sequence of PatE conventionally known as the leader sequence. For example, as the leader sequence, a sequence such as MKEQNSFNLLQEVTESELDLILGA derived from another peptide (Lacticin 481 precursor), a sequence such as MILASLSTFQQMWISKQEYDEAGDA derived from human actin, or a sequence such as MELQLRPSGLEKKQAPISELNIAQTQGGDSQVLALNA obtained by shuffling the leader sequence of PatE.
As the leader sequence, a sequence having high helicity (α helicity) may be used.
In the phrase “in the presence of a peptide comprising a leader sequence of a substrate of the azoline backbone-introducing enzyme” as used herein, the peptide may be, in the reaction system, present as an independent peptide from the precursor peptide comprising the recognition sequence 1, -(Xaa1-Xaa2)n-, and the recognition sequence 2 or have been fused with the precursor peptide comprising the recognition sequence 1, -(Xaa1-Xaa2)n-, and the recognition sequence 2.
In the substrate of natural PatD, the leader sequence, recognition sequence 1, cassette sequence, and recognition sequence 2 are fused with each other, but as will be shown later in Examples, the present inventors have found that in reacting the precursor peptide comprising the recognition sequence 1, —(Xaa1-Xaa2)n-, and the recognition sequence 2 with the azoline backbone-introducing enzyme, the precursor peptide may become a substrate of the azoline backbone-introducing enzyme even if the leader sequence is added to the reaction system as an independent peptide.
When the leader sequence is allowed to exist as a peptide independent from the precursor peptide comprising the recognition sequence 1, -(Xaa1-Xaa2)n-, and the recognition sequence 2, each of these peptides (that is, the peptide comprising the leader sequence and the precursor peptide) becomes shorter, which makes preparation easy. When the leader sequence is fused to the precursor peptide, the leader sequence is desirably cleaved therefrom prior to screening, because there is a possibility of causing steric hindrance when the peptide is bound to a target molecule. When the peptide comprising the leader sequence is originally allowed to exist as a peptide independent from the precursor peptide, cleaving of it therefrom is not necessary.
These two peptides may be prepared by either translational synthesis or chemical synthesis.
Examples of the azoline backbone-introducing enzyme include PatD and enzymes having homology therewith. As the enzyme having homology with PatD, those included in the report of Lee, etc. (Lee, S. W. et al., PNAS vol. 105, No. 15, 5879-5884, 2008) may be used, but it is not limited to them.
The azoline backbone-introducing enzyme may be extracted/purified from microorganisms producing the azoline backbone-introducing enzyme or may be expressed by gene recombination. For example, an azoline backbone-introducing enzyme can be expressed in Escherichia coli as a construct having at the N-terminus thereof a His tag and purified by making use of the His tag according to a conventional manner. The azoline backbone-introducing enzyme may be a mutant thereof insofar as it has an azoline backbone introducing ability.
The reaction between the azoline backbone-introducing enzyme and the peptide library can be conducted by adding the azoline backbone-introducing enzyme in the container in which the precursor peptide was expressed, that is, in one pot without purifying the precursor peptide. The reaction between the azoline backbone-introducing enzyme and the peptide library can be conducted under appropriate conditions selected by those skilled in the art and for example, when the azoline backbone-introducing enzyme is PatD, the conditions are selected within a range of a final concentration of from 0.1 μM to 50 μM, a reaction temperature of from 4° C. to 45° C., and a reaction time of from 5 minutes to 100 hours.
Confirmation of the reaction can be conducted by measuring a mass change by using, for example, MALDI-TOF MS.
As the construction method of an azoline compound library according to one embodiment of the present invention, when the leader sequence is fused with the precursor peptide comprising the recognition sequence 1, -(Xaa1-Xaa2)n-, and the recognition sequence 2, a step of cleaving the leader sequence from the precursor peptide may be conducted. This facilitates binding of a cassette domain portion represented by -(Xaa0)m- to a target substance.
Cleavage of the leader sequence can also be conducted by adding a peptidase in the container where the reaction of the azoline backbone-introducing enzyme was conducted.
Cleavage of the leader sequence may be conducted by cleaving in the middle of the leader sequence, in the middle of the recognition sequence 1, at the binding site between the leader sequence and the recognition sequence 1, at the binding site between the recognition site 1 and the cassette domain, and at the binding site between the cassette domain and the recognition site 2. The kind of a peptidase may be selected depending on the sequence at the cleavage site. Examples of the peptidase include, but not limited to, trypsin, Glu-C, Lys-C, Asp-N, Lys-N, Arg-C, thrombin, Factor Xa, prescission protease, TEV protease, entherokinase, and HRV 3C Protease.
As one example, when GLEAS is used the recognition sequence 1 of the azoline backbone-introducing enzyme, endoproteinase Glu-C can be used and cleaving is conducted between Glu and Ala. The reaction of Glu-C can be conducted in a known manner.
In one embodiment of the construction method of an azoline compound library according to the present invention, an azoline compound library containing at least two complexes between an azoline compound and an mRNA encoding the peptide represented by the formula (I) is constructed. This makes it possible to apply the azoline compound library to mRNA display (Nemoto, N. et al., FE BS Lett. 1997, 405-408; Roberts, R. W. and Szostak, J. W. Proc. Natl. Acad. Sci. USA 1997, 94, 12297-12302).
By using such an azoline compound-mRNA complex library and conducting screening of an azoline compound that binds to a target substance, it is possible to obtain a cDNA-containing complex by a reverse transcription reaction of the azoline compound-mRNA complex selected and determine the base sequence of it.
The azoline compound-mRNA complex can be prepared, for example, by binding puromycin to the 3′ end of each of mRNAs of the mRNA library in a known manner to prepare a puromycin-bound mRNA library and expressing a precursor peptide in a cell-free translation system by using this puromycin bound mRNA library.
After preparation of the peptide-mRNA complex library in such a manner, it is reacted with PatD and then a leader sequence is cleaved if necessary to obtain an azoline compound library.
In the construction method of an azoline compound library according to one embodiment of the present invention, at least one of peptides represented by the formula (I) has at least one of the following characteristics (i) to (iv):
(i) m represents from 2 to 40 (with the proviso that 7 and 8 are excluded) and m is, for example, 2, 3, 4, 5, 6, 9, 10, 12, 14, 16, 20, 30, or 40;
(ii) n represents from 1 to 20 (with the proviso that 3 and 4 are excluded) and n is, for example, 1, 2, 5, 6, 7, 8, 10, 15, or 20;
(iii) at least one, at least two, at least three, at least four, or at least five of Xaa1s is (are) an amino acid selected from Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof; and
(iv) at least one, at least two, at least three, at least four, or at least five of Xaa1s is (are) a hydrophilic amino acid.
Peptides having at least one of the characteristics of (i) to (iv) include peptides which have conventionally been considered unsuitable as a substrate of the azoline backbone-introducing enzyme such as PatD and the present inventors have confirmed, for the first time, that they become a substrate of the azoline backbone-introducing enzyme.
The following are cassette sequences confirmed for the first time as a substrate of the azoline backbone-introducing enzyme.
In the construction method of an azoline compound library according to one embodiment of the present invention, at least one of the azoline compounds has 5 or more azoline backbones.
It has conventionally been considered that 5 or more azoline backbones can not be introduced into the cassette domain of natural PatE even if an azoline backbone-introducing enzyme is used. The present inventors for the first time succeeded in synthesis of an azoline compound having 5 or more azoline backbones.
In one embodiment of the construction method of an azoline compound library according to the present invention, at least one of the azoline compounds has an azoline backbone other than ordinary oxazoline/thiazoline obtained from Ser/Thr/Cys.
It has conventionally been considered that an azoline backbone is not introduced into an amino acid other than Ser, Thr, and Cys present in the cassette domain of natural PatE even if an azoline backbone-introducing enzyme is used. The present inventors have for the first time synthesized compounds in which an imidazoline backbone or a substituted azoline backbone derived from non-protein amino acids such as Dap, tBuSer, iPrSer, PhSer, and EtSer has been introduced using an azoline backbone-introducing enzyme such as PatD.
The construction method of an azoline compound library according to one embodiment of the present invention includes a step of macrocyclizing an azoline compound before or after cleavage of the leader sequence. Macrocylization of an azoline compound can be conducted in a known method of macrocyclizing a peptide or a method equivalent thereto. For example, it can be conducted in accordance with the method disclosed in WO2008/117833 or the method of Timmerman, et al. (Timmerman, P et al., ChemBioChem 2005, 6: 821-824).
The present invention also provides a construction method of an azole compound library containing two or more azole compounds. Of the terms used in the construction method of an azole compound library according to the present invention, those also used in the above-mentioned construction method of an azoline compound library are regarded as having the same meanings unless otherwise particularly specified.
The term “azole compound” as used herein means a compound having an azole backbone introduced into at least one of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof of a peptide represented by the following formula (I):
A-(Xaa0)m-B (I)
[wherein, m numbers of Xaa0s represent arbitrary amino acids, at least one of which is an amino acid selected from the group consisting of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof, m represents an integer selected from 2 to 20, and A and B each independently represents a peptide composed of from 0 to 8 amino acids).
In one embodiment of the present invention, the azole compound is a compound of the formula (I) in which -(Xaa0)m- is -(Xaa1-Xaa2)n-
[wherein, n numbers of Xaa1 each independently represent an arbitrary amino acid, n numbers of Xaa2 each independently represent an amino acid selected from the group consisting of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof, and n represents an integer selected from 1 to 10].
The Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof into which the azole backbone has been introduced may be either at a position of Xaa1 or at a position of Xaa2.
The term “introducing an azole backbone into at least one of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof” as used herein means that an oxidation reaction of an azoline ring produced by the dehydration reaction of Cys, Ser, or Thr proceeds to introduce an azole ring represented by the following formulas:
Introduction of an azole backbone into Ser, Thr, Cys, or 2,3-diamino acid produces an oxazole, thiazole, or imidazole backbone as follows:
For example, introduction of an azole backbone into the above-mentioned artificial Thr analog residue produces the following oxazole backbone.
Introduction of an azole backbone into the above-mentioned artificial Cys analog residue produces the following thiazole backbone.
Introduction of an azole backbone into the above-mentioned artificial diamino acid analog residue produces the following imidazole backbone.
In the construction method of an azole compound library according to one embodiment of the present invention, an azoline backbone-introducing step in the above-mentioned construction method of an azoline compound library is followed by a step of reacting the library having azoline backbones introduced therein with an azole backbone-introducing enzyme to convert at least one of the azoline backbones into an azole backbone. The oxazoline backbone introduced into Ser or Thr, the thiazoline backbone introduced into Cys, and an imidazoline backbone introduced into 2,3-diamino acid are converted into an oxazole backbone, a thiazole backbone, and an imidazole backbone, respectively. The step of reacting the library having an azoline backbone introduced therein with the azole backbone-introducing enzyme may be conducted in the presence of a peptide comprising a leader sequence of a substrate of the azole backbone-introducing enzyme. The peptide comprising a leader sequence of a substrate of the azole backbone-introducing enzyme may be the same as or different from the peptide comprising a leader sequence of a substrate of the azoline backbone-introducing enzyme.
Examples of the azole backbone-introducing enzyme include PatG and enzymes having homology therewith. Examples of the enzymes having homology with PatG include, but not limited to, those included in the report of Lee, et al. (Lee, S. W. et al., PNAS vol. 105, No. 15, 5879-5884, 2008).
The reaction with the azole backbone-introducing enzyme can be conducted by adding the azole backbone-introducing enzyme in the container in which the reaction with the azoline backbone-introducing enzyme has been conducted.
In the construction method of an azole compound library according to one embodiment of the present invention, a mutant obtained by deleting a peptidase domain from PatG or a mutant which has lost its peptidase activity by point mutation is used as the azole backbone-introducing enzyme. PatG is comprised of two domains and in natural one, an oxidase domain at the N-terminus is involved in conversion of an azoline backbone constructed by PatD into an azole backbone, while a peptidase domain at the C-terminus is involved in cleaving of the peptide site and macrocyclization after modification. Accordingly, in the construction method of an azole compound library according to the present invention, a peptidase domain-deficient mutant or a mutant that has lost its peptidase activity as a result of point mutation can be used.
The present invention also provides an azoline compound library containing two or more azoline compounds. Of the terms used here, those also used in the above-mentioned construction method of a library are regarded as having the same meanings unless otherwise particularly specified.
The azoline compound library according to one embodiment of the present invention includes at least one of azoline compounds having at least one of the following characteristics (i) to (iv):
(i) m represents from 2 to 20 (with the proviso that 7 and 8 are excluded) and m is, for example, 2, 3, 4, 5, 6, 9, 10, 12, 14, 16, 20, 30, or 40;
(ii) n represents from 1 to 10 (with the proviso that 3 and 4 are excluded) and n is, for example, 1, 2, 5, 6, 7, 8, 10, 15, or 20;
(iii) at least one, at least two, at least three, at least four, or at least five of Xaa1s is (are) an amino acid selected from Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof; and
(iv) at least one, at least two, at least three, at least four, or at least five of Xaa1s is (are) a hydrophilic amino acid.
Peptides having at least one of the characteristics of (i) to (iv) include peptides which have conventionally been considered unsuitable as a substrate of the azoline backbone-introducing enzyme such as PatD and the present inventors have confirmed for the first time that they become a substrate of the azoline backbone-introducing enzyme.
In the azoline compound library according to one embodiment of the present invention, azoline compounds each constitute a complex with mRNA encoding the peptide portion thereof. The library may be applicable to mRNA display.
In the azoline compound library according to one embodiment of the present invention, the entirety or a portion of the recognition sequence by the azoline backbone-introducing enzyme may have been bound to the N-terminus and C-terminus of the peptide represented by the formula (I).
The recognition sequence of the azoline backbone-introducing enzyme is necessary for modifying the peptide, which has been expressed in a cell-free translation system, with the azoline backbone-introducing enzyme. When an azoline compound library is constructed using the method of the present invention and the leader sequence is cleaved using a peptidase, the entirety or a portion of these sequences may remain at the N-terminus and C-terminus.
For example, supposing that the recognition sequence 1 is GLEAS (SEQ ID NO: 3) and the leader sequence is cleaved using Glu-C, Ala-Ser remains on the N-terminus side of the cassette domain.
The present invention also provides an azole compound library containing two or more azole compounds. Of the terms used here, those also used in the above-mentioned construction method of a library are regarded as having the same meanings unless otherwise particularly specified.
The azole compound library according to one embodiment of the present invention includes at least one of azole compounds having at least one of the following characteristics (i) to (iv):
(i) m represents from 2 to 20 (with the proviso that 7 and 8 are excluded) and m is, for example, 2, 3, 4, 5, 6, 9, 10, 12, 14, 16, 20, 30, or 40;
(ii) n represents from 1 to 10 (with the proviso that 3 and 4 are excluded) and n is, for example, 1, 2, 5, 6, 7, 8, 10, 15, or 20;
(iii) at least one, at least two, at least three, at least four, or at least five of Xaa1s is (are) an amino acid selected from Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof; and
(iv) at least one, at least two, at least three, at least four, or at least five of Xaa1s is (are) a hydrophilic amino acid.
Peptides having at least one of the characteristics (i) to (iv) include peptides which have conventionally been considered unsuitable as a substrate of the azoline backbone-introducing enzyme such as PatD and the present inventors have confirmed for the first time that they become a substrate of the azoline backbone-introducing enzyme. It is therefore understood that an azole backbone may be introduced by introducing an azoline backbone by using the azoline backbone-introducing enzyme and then conducting modification with the azole backbone-introducing enzyme.
In the azole compound library according to one embodiment of the present invention, the azole compounds each constitute a complex with mRNA encoding the peptide portion thereof. The library may be applicable to mRNA display.
In the azole compound library according to one embodiment of the present invention, the entirety or a portion of the recognition sequence of PatD may have been bound to the N-terminus and C-terminus of the peptide represented by the formula (I).
The recognition sequence of PatD is necessary for modifying the peptide, which has been expressed in a cell-free translation system, with PatD. When an azole compound library is constructed using the method of the present invention and the leader sequence is cleaved using a peptidase, the entirety or a portion of these sequences may remain at the N-terminus and C-terminus.
For example, supposing that the recognition sequence 1 is GLEAS and the leader sequence is cleaved using Glu-C, Ala-Ser remains on the N-terminus side of the cassette domain.
The present invention provides a screening method for identifying an azoline compound that binds to a target substance.
The screening method according to one embodiment of the present invention includes a step of bringing the azoline compound library constructed by the construction method of the present invention or the azoline compound library according to the present invention into contact with a target substance; and incubating the resulting compound.
The target substance is not particularly limited herein and may be, for example, a small molecular compound, a high molecular compound, a nucleic acid, a peptide, a protein, or the like. In particular, according to the library of the present invention, a target substance having a protease activity can also be used.
The target substance, for example, immobilized on a solid phase support may be brought into contact with the library of the present invention. The “solid phase support” to be used herein is not particularly limited insofar as it is a carrier onto which a target substance can be immobilized and examples include microtiter plates, a substrate and beads made of glass, a metal, a resin, or the like, nitrocellulose membrane, nylon membrane, and PVDF membrane. The target substance can be immobilized onto such a solid phase support in a known manner.
The target substance and the library may be brought into contact with each other in a buffer selected as needed and reacted while controlling pH, temperature, time, or the like.
The screening method according to one embodiment of the present invention may further include a step of selecting the azoline compound bound to the target substance. The azoline compound may be labeled using a known method capable of detectably labeling peptides before it is bound to the target substance. After the step of bringing them into contact, the surface of the solid phase support may be washed with a buffer to detect the azoline compound which has bound to the target substance.
Examples of the detectable label include enzymes such as peroxidase and alkaliphosphatase, radioactive substances such as 125I, 131I, 35S, and 3H, fluorescent substances such as fluorescein isothiocyanate, rhodamine, dansyl chloride, phycoerythrin, tetramethyl rhodamine isothiocyanate, and infrared fluorescent materials, light-emitting substances such as luciferase, luciferin, and aequorin, and nanoparticles such as gold colloid and quantum dot. When the label is an enzyme, the azoline compound can be detected by adding a substrate of the enzyme to develop a color. The peptide may also be detected by binding biotin thereto and then binding avidin or streptavidin labeled with an enzyme or the like to the biotin-bound peptide.
It is possible not only to detect or analyze the presence/absence or degree of binding but also to analyze the enhanced or inhibited activity of the target substance and thereby identify an azoline compound having such enhancing or inhibitory activity. Such a method makes it possible to identify an azoline compound having physiological activity and useful as a pharmaceutical.
When the azoline compound library is comprised of azoline compound-mRNA complexes, after an azoline compound bound to a target substance is selected by the above-mentioned method, a step of analyzing the base sequence of the mRNA of the azoline compound thus selected may be conducted.
The analysis of the base sequence of mRNA can be conducted by synthesizing cDNA by using a reverse transcription reaction and then, analyzing the base sequence of the resulting cDNA. This makes it possible to easily specify the relationship between a genotype and a phenotype.
An azoline compound having strong binding ability to the target substance may be concentrated by conducting transcription further after the reverse transcription reaction to convert the library into the mRNA library again, and repeating screening with the target compound.
The present invention provides a screening method for identifying an azole compound that binds to a target substance.
The screening method according to one embodiment of the present invention may include a step of bringing the azole compound library constructed using the construction method of an azole compound library according to the present invention or the azole compound library according to the present invention into contact with a target substance, followed by incubation.
The screening method of an azole compound can be conducted in accordance with the above-mentioned screening method of an azoline compound.
The present invention provides a screening kit of an azoline compound or azole compound.
The screening kit according to one embodiment of the present invention includes an azoline compound library or azole compound library constructed by the construction method of the present invention or the azoline compound library or azole compound library according to the present invention. The screening kit of the present invention includes, in addition, a reagent and an apparatus necessary for detecting the binding between a target substance and an azoline compound or azole compound. Examples of such a reagent and apparatus include, but not limited to, solid phase supports, buffers, labeling reagents, enzymes, enzyme reaction terminator solutions, and microplate readers.
In the screening kit of the present invention, the library may be immobilized in array form on a solid phase support.
The present invention provides a method of preparing an azoline compound in which at least one azoline backbone has been introduced into at least one of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof of Xaa0 of a peptide represented by the formula (I).
This method includes:
a step of preparing an mRNA encoding a precursor peptide having, in order of mention from the N-terminus, a recognition sequence 1 by an azoline backbone-introducing enzyme, -(Xaa0)m-, and a recognition sequence 2 by an azoline backbone-introducing enzyme (the recognition sequences 1 and 2 meaning recognition sequences by an azoline backbone-introducing enzyme composed of from 0 to 10 amino acids);
a step of expressing a precursor peptide in a cell-free translation system by using the above-mentioned mRNA; and
a step of reacting the azoline backbone-introducing enzyme and the precursor peptide in the presence of a peptide having a leader sequence of a substrate of the azoline backbone-introducing enzyme to introduce an azoline backbone into at least one of Cys, Ser, Thr, and 2,3-diamino acid, and analogs thereof of Xaa0.
The peptide having a leader sequence and the precursor peptide having a recognition sequence 1, -(Xaa0)m-, and a recognition sequence 2 are separate peptides.
According to this method, the peptide having a leader sequence and the precursor peptide having a recognition sequence 1, -(Xaa0)m-, and a recognition sequence 2 may be made shorter, respectively, so that they can be prepared easily. For the preparation, chemical synthesis, translational synthesis and combination of them can be employed. Prior to screening, separation of the leader sequence is not necessary.
The present method is therefore particularly advantageous when an azoline compound that binds to a target substance is identified by using the screening method of the present invention and then, the azoline compound is mass produced.
The present invention embraces a preparation method of an azole compound by using the azoline compound obtained using the above-mentioned preparation method of an azoline compound.
The present method includes a step of reacting an azoline compound and an azole backbone-introducing enzyme in the presence of a peptide having a leader sequence of a substrate of the azole backbone-introducing enzyme and thereby converting at least one of azoline backbones into an azole backbone.
According to the present method, preparation of an azole compound may be easily prepared because the peptide comprising a leader sequence and the azoline compound may each be made shorter. The preparation may be conducted using chemical synthesis, translational synthesis, or combination of them. In addition, prior to screening, separation of the leader sequence is not necessary.
The present method is therefore particularly advantageous for, after identification of an azole compound that binds to a target substance, mass production of the azole compound.
The kit for preparing an azoline compound or an azole compound according to the present invention serves to prepare an azoline compound or azole compound by using the above-mentioned method so that it includes an azoline backbone-introducing enzyme or azole backbone-introducing enzyme and a peptide having a leader sequence of a substrate of the azole backbone-introducing enzyme.
In addition, the present kit may include necessary reagents and instruments, an instruction manual, and the like.
The present invention will next be described more specifically based on Example. It should however be borne in mind that the present invention is not limited to or by the Example.
Synthesis scheme of an azoline compound library in the following Example is shown in
A PatD gene was inserted into a pET16b plasmid to prepare a construct plasmid containing at the N-terminus thereof a 10×His tag. It was transformed into an E. coli BL21(DE3)pLysS strain, followed by culturing at 30° C. When O.D. reached 0.4, 0.1 mM of IPTG was added to induce expression, followed by culturing overnight at 16° C. The cells collected were suspended in a lysis buffer (1 M NaCl, 10 mM Imidazole, 50 mM HEPES-Na (pH7.5)) and then lysed ultrasonically. The sample was filtered and purified using a His-Trap HP column. The column was equilibrated in advance with 10 CV of Buffer A (500 mM NaCl, 25 mM imidazole, 50 mM HEPES-Na (pH7.5)) and after injection of the sample therein, the protein was eluted from the column by gradually increasing the concentration of Buffer B (500 mM NaCl, 500 mM imidazole, 50 mM HEPES-Na (pH7.5)) to obtain a pure PatD fraction. The sample thus obtained was concentrated to about 4 times with Amicon Ultra (Millipore) 30 kDa. Then, buffer was exchanged with Storage Buffer (200 mM NaCl, 25 mM HEPES (pH7.5), 10% glycerol) by using PD-10 (GE Lifescience) and the resulting sample was stored at −80°.
[2] Construction of PatE Plasmid (pET16b)
The following PatE sequence was subcloned into pET16b.
DNA of PatEpre was prepared by conducting PCR twice with the PatE plasmid as a template. The underlined portion is DNA encoding GLEAS (SEQ ID NO: 3) of the recognition sequence 1. The region from position 48 to position 153 of SEQ ID NO: 59 is a code region of the leader sequence.
PatEpre encodes a peptide composed of the following amino acid sequence having the leader sequence and the recognition sequence (underlined portion).
Primers used for PCR of PatEpre are shown in the following table. The sequence of the primers is shown in a primer list which will be shown later.
A mutant DNA having mutation in the cassette domain thereof was prepared by conducting PCR twice or three times with PatEpre as a template. The peptide thus obtained had the following sequence:
The sequence in (XXX) corresponding to the cassette domain and primers used are shown below. The sequence of the primers is shown in the primer list which will be described later.
FT
TFC
FT
TACITFC
indicates data missing or illegible when filed
[3-2-2] Peptides Other than Those Having AYDGVEPS (SEQ ID NO: 5) as Recognition Sequence 2
Similarly, PCR was conducted twice or three times with PatEpre2 as a template and DNA of a peptide having, as a C-terminus sequence, a sequence other than AYDGVEPS was also prepared.
The (XXX) represents a cassette domain and the (YYY) represents a recognition sequence 2.
Sequence
Sequence
indicates data missing or illegible when filed
Primers used for DNA preparation were shown below. The sequence of the primers was shown in the primer list which will be shown later.
After the DNA prepared in 3-2 was transcribed and translated in a cell-free protein expression system of 2.5 μl scale in accordance with the method of Kawakami, et al. (Kawakami et al., Chemistry & Biology 15, 32-42 (2008)) and the solution conditions were adjusted by adding 40 mM Tris-HCl (pH 8.0), 8 mM DTT, 4 mM MgCl2, and 0.8 mM ATP (each, final concentration), recombinant PatD was added.
The reaction was conducted under two conditions as described below.
The mass of the peptide was measured using MALDI-TOF-MS by using sinapinic acid as a matrix and whether a mass change occurred or not by the addition of PatD was checked. The number of azoline rings introduced can be found from the mass change.
The results of mass spectroscopy at the time when C1wt whose amino acid sequence in the cassette domain was the same as that of wild type PatE was modified with PatD are shown in
The results of C1m10 whose cassette domain was composed of 12 amino acids (in the formula (I), n=6) and C1m38 whose cassette domain was composed of 16 amino acids (in the formula (I), n=8) are shown in
Other typical results are shown in
The substrate tolerance of PatD confirmed based on the results of such a test is shown in
After the PatD enzyme reaction, 0.5 μg of Glu-C (Roche) was added to 5.0 μl of the reaction solution. The resulting mixture was incubated at 25° C. for 2 hours to cleave the peptide. The mass spectrometry analysis of the modified peptide which had been obtained as a result of such a test and from which the leader sequence had been cleaved are shown in
[7] Mass Spectroscopy after Glu-C Enzyme Reaction
With α-CHCA as a matrix, the mass of the peptide was measured using MALDI-TOF-MS and formation of a peptide from which the leader sequence had been cleaved was confirmed.
An example of the results is shown in
DNA of PatEpre2 having a non-translation region suited for construction of a library was prepared. The underlined portion is a DNA encoding GLEAS (SEQ ID NO: 3), the recognition sequence 1. The sequence from position 46 to position 151 of SEQ ID NO: 61 is a code region of the leader sequence.
With PatEpre2 as a template, two libraries as described below were constructed by conducting PCR twice or three times by using a primer containing a random base sequence.
A double-stranded DNA having the following sequence was prepared. (n=3 to 8)
GT
Translation of this DNA results in synthesis of the following peptide:
DGVGSGSGS
A double-stranded DNA having the following sequence was prepared. (n=3 to 6)
GT
Translation of this DNA results in synthesis of the following peptide.
The primers used for the construction of individual libraries are shown below. The sequences of the primers are shown in the primer list shown below.
Tests were conducted in a similar manner to that described above in [1] to [8] in order to study the necessity of a leader sequence: by removing a leader sequence from a substrate peptide; by adding a leader sequence obtained by translational synthesis as a peptide separate from a substrate peptide and adding it to a reaction system; or by adding a leader sequence obtained by chemical synthesis to give a final concentration of 1 uM, 10 uM, or 50 uM. The cassette sequence was comprised of 8 amino acids (VTACITFC).
The results are shown in
In a similar manner to that employed above in [1] to [8], a portion of a leader sequence was deleted as shown in
As shown in
In a similar manner to that described above in [1] to [8], the entirety of the leader sequence was substituted with a completely different peptide sequence as shown in
As shown in
In a similar manner to that employed above in [1] to [8], the enzyme activity by PatD was confirmed by introducing point mutation into some amino acids of the leader sequence as shown in
As shown in
In a similar manner to that employed above in [1] to [8], enzyme activity by PatD was studied by deleting a recognition sequence, by changing the sequence, or by adding another sequence as shown in
As shown in
These results have suggested that the modification efficiency with PatD becomes higher when the recognition sequence 1 is present, but no particular limitation is imposed on its sequence and the presence or absence of the recognition sequence 2 has almost no influence on the modification efficiency with PatD. They have also suggested that the addition of a sequence to the downstream of the recognition sequence 2 has almost no influence on the modification efficiency.
[14] Study on Modification Efficiency, with PatD, of a Substrate Having, in the Cassette Sequence Thereof, a Non-Natural Amino Acid
As shown in
Substrates having the following sequences were synthesized, respectively and modification with PatD was confirmed. The results are shown in the following table. Typical results are shown in
indicates data missing or illegible when filed
[16] Screening Using mRNA Display Method
Compounds that bound to matrix metalloproteinase (MMP) 12 were screened in accordance with an mRNA display method by using the azoline compound library obtained using the above-mentioned method.
MMP12 was expressed in Escherichia coli as a construct having, at the C-terminus thereof, a 6×His tag and an Avi tag. Purification was conducted by making use of the His tag.
Since the Avi tag was biotinylated with BirA expressed by birA incorporated in the same plasmid, it was added for immobilization of MMP12 with streptavidin beads upon mRNA display.
[16-2] Construction of mRNA Library
The DNA library obtained in [8] was transcribed using T7 RNA polymerase to obtain an mRNA corresponding to the library.
[16-3] mRNA Display
A cycle from “Ligation with puromycin linker” to “amplification of sequence information of peptide thus recovered” described below was repeated and peptides binding to MMP12 were selected from the azoline-containing compound library.
[16-3-1] Ligation with Puromycin Linker
The puromycin linker represented by the below-described sequence was annealed with the above-mentioned mRNA library and ligated to each other via a T4 RNA ligase. (SPC18 represents PEG having C and O in the total number of 18)
The mRNA library to which the puromycin linker had been ligated was translated and a peptide library was synthesized. Puromycin reacts to the C-terminus of the peptide thus synthesized, by which the mRNA and the peptide are connected to each other.
The peptide library tagged with mRNA was subjected to post-translational modification with PatD to introduce azoline rings in the cassette sequence.
The mRNA bound to the peptide was reverse transcribed and (azoline-modified peptide)-mRNA-DNA complexes were synthesized.
Glu-C was added and the leader sequence was cleaved.
[16-3-6] Selection of Azoline-Modified Peptide that Binds to MMP12
MMP12 immobilized onto streptavidin beads was mixed with the azoline-containing compound library prepared above and the mixture was incubated at 4° C. for 30 minutes. The supernatant was removed and the residual beads were washed with a buffer. A PCR solution was added to the beads, the mixture was heated at 95° C. for 5 minutes, the peptide was eluted from the beads, and the supernatant was recovered.
The DNA contained in the (azoline-modified peptide)-mRNA-DNA complex which had bound to MMP12 and been recovered was amplified by PCR. The DNA thus obtained was transcribed into a corresponding mRNA.
The above-mentioned series of operations was repeated. When a change in the recovery ratio of DNA stopped, TA cloning was conducted using the amplified DNA and the sequence of the resulting azoline-containing compound was identified.
A series of operations was conducted by using not mRNA from the mRNA library but mRNA of the selected peptide in accordance with a scheme of mRNA display and whether the selected azoline-containing compound binds to MMP12-immobilised beads was studied. In addition, such operations were conducted under the condition wherein post-translational modification with PatD is performed or the condition wherein the modification is not performed. The results have suggested that the sequences thus obtained bind to MMP12 when they have been modified with PatD and that, in these sequences, the azoline backbone contributes to binding to MMP12.
The outline of the mRNA display method is shown in
The results of selection are shown in
The sequences of five azoline-containing compounds A to E selected based on the results of selection were analyzed (not including data) and evaluation results of the binding ability to MMP12 are shown in
A list of base sequences of the primers used is shown below.
indicates data missing or illegible when filed
SEQ ID NO: 1 represents the amino acid sequence of the leader sequence of PatE.
SEQ ID NOS: 2 and 3 are examples of the recognition sequence 1 by an azoline backbone-introducing enzyme, respectively.
SEQ ID NOS: 4 to 9 are examples of the recognition sequence 2 by an azoline backbone-introducing enzyme, respectively.
SEQ ID NOS: 10-57 are amino acid sequences confirmed newly to become a substrate of an azoline backbone-introducing enzyme.
SEQ ID NO: 58 is the base sequence of a nucleic acid encoding PatE.
SEQ ID NO: 59 is the base sequence of a nucleic acid encoding PatEpre.
SEQ ID NO: 60 is the amino acid sequence of the cassette domain of wild type PatE.
SEQ ID NO: 61 is the base sequence of a nucleic acid encoding PatEpre2.
SEQ ID NO: 62 is the base sequence of a nucleic acid encoding the peptide portion of each compound of (XC)n library.
SEQ ID NO: 63 is an amino acid sequence of the peptide portion of each compound of (XC)n library.
SEQ ID NO: 64 is the base sequence of a nucleic acid encoding the peptide portion of each compound of (X—C/S/T)n library.
SEQ ID NO: 65 is the amino acid sequence of the peptide portion of each compound of (X—C/S/T)n library.
SEQ ID NOS: 66 to 172 are the base sequences of primers used in Examples of the present application.
| Number | Date | Country | Kind |
|---|---|---|---|
| 2011-052219 | Mar 2011 | JP | national |
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/JP2012/056181 | 3/9/2012 | WO | 00 | 11/15/2013 |
