NZ715706B2 - 3-aryl propiolonitrile compounds for thiol labeling - Google Patents

Abstract

The present invention relates to a process for labeling compounds comprising thiol moieties with 3-arylpropiolonitrile compounds, to 3-arylpropiolonitrile compounds substituted with tag moieties and to specific 3-arylpropiolonitrile linkers.

Description

-aryl propiolonitrile compounds for thiol labeling The t invention relates to a process for labeling compounds comprising thiol moieties with 3—ary1propiolonitrile compounds, to 3-arylpropiolonitrile compounds substituted with tag moieties and to c 3-arylpropiolonitrile linkers.

Background of the invention Over 90% of the human proteins contain cysteines, while in silico digest of the human proteome revealed that only about 15% of all human tryptic peptides detectable by mass spectroscopy (MS) contain at least one cysteine in their sequence. This observation combined with the presence of a highly reactive thiol group on its side chain makes cysteine an attractive target for chemical labeling. Cysteine is the only coded amino acid that carries a nucleophilic sulfhydryl (or thiol) group (-SH), which largely exceeds the reactivity of any other nucleophilic function susceptible to be present in proteins. As a result, chemospecific cysteine tization is by far the most widely used method for al tagging of proteins. Among the vast number of al cysteine ation s reported in literature so far, reagents such as N—substituted maleimides, 4-vinylpyridines and iodoacetamides are most ly used. All of them s drawbacks ting them from being ideal methodology for cysteine labeling, though being suited for this task. These drawbacks are mainly presence of undesired side reactions, in particular for iodoacetamides and maleimides, and instability of addition product in biological environments due to reversible thiol exchange and other side reactions.

The present invention relates to a process for labeling compounds comprising at least one thiol moiety, such as cysteine, with nds comprising a tag moiety and a 3- arylpropiolonitrile moiety. Said compounds and their addition products with cysteine derivatives show an unexpected stability in a wide range of conditions. The process for ng compounds comprising thiol moieties of the invention can thus be used for a wide range of applications.

WO 20151001117 2 2014/064387 Summam of the invention The first object of the invention is a process for the preparation of a labelled compound comprising a thiol moiety, comprising ting a compound comprising a thiol moiety with a compound of formula (I) wherein R1 to R5 are as described below, and wherein at least one of R1 to R5 comprises a tag moiety.

Another object of the invention is a compound of formula (I) wherein R1 to R5 are as defined below, and wherein at least one of R1 to R5 comprises a tag moiety.

Another object of the invention is a nd of formula (II) wherein R1 to R5 are as defined below, and wherein at least one of R1 to R5 is different from a hydrogen atom.

Another object of the invention is a compound of formula (111) R2 R1 S—Re wherein R6-S corresponds to the moiety of the compound comprising at least one thiol moiety as identified above.

WO 20151001117 3 Brief description of the figures Fig l: Evolution of intensity of fluorescence over time obtained in human plasma for the same concentration of compounds A and B.

Fig 2: a) Evolution of intensity of fluorescence over time obtained in cellula for the same concentration of compounds A and B. b) Intensity ratio compound B/compound A at different times in cellulo. c) Microscope pictures of cells treated with compounds A and B, superimposition of TAMRA and Hoechst ng. White spots around nucleus correspond to hydrolyzed probe. A — arylpropiolonitrile probe, B — maleimide probe.

Fig 3: HPLC monitoring of the hydrolysis of phenylmaleimide (2) in PBS (lx, pH 7.6) at lmM concentration at 25°C; the peaks correspond, from the earliest to the O \ (3%” O WH N 0 O , COOH, and 2O latest, to ; conversion was monitored by earance of the starting material (a). Pseudo first order rate constant for the reaction was determined by ng the ln([phenylmaleimide]) versus time and analyzing by linear regression. The constant corresponds to the te value of determined slope (b).

Fig 4: HPLC monitoring of hydrolytic stability of N—(4-(cyanoethynyl)phenyl)acetamide -APN, 11) in PBS (lx, pH 7.6) at lmM concentration at 25°C. sion was monitored by disappearance of the starting material; the peaks correspond, from the st to the latest, to AcN : :N and 11 .

. No detectable convers1on of arylpropiolonitrile 11 was observed after 5 hours of monitoring.

Fig 5: MTT test results for compounds 1, 2, 3, 5, 7, 11, 10 and 9.

Fig 6: a) tic structure and measured DLS spectra of CD38 and CD38 A275C mutant; b) scheme of CD38 A275C modification with 49; c) DLS (Dynamic Light Scattering) spectrum of the resulting conjugate.

Fig 7: Gel ophoresis of CD38-C375 mutant labeled with a compound according to the invention and with the corresponding maleimide compound, before ation (a) and after purification (b).

Fig 8: Strategy of preparation of the antibody-TAMRA conjugate with a compound ing to the invention, and the comparison with the corresponding maleimide.

Fig 9: Gel electrophoresis of the conjugates obtained respectively with the compound according to the invention (CBTF) and with the corresponding maleimide (SMCC).

Fig lO:Mass spectrum for the conjugate obtained with the compound according to the invention.

Fig ll:Zoom on the mass spectrum of figure 10.

Fig 12:Mass spectrum obtained with the maleimide.

Fig l3:Zoom on the mass um of figure 12.

Fig l4:General scheme of direct conjugation of the compound 58 to partially reduced Trastuzumab.

Fig 15:SDS-PAGE analysis of the obtained conjugates shows that compound 58 is covalently attached to the antibody Fig 16: General scheme of rebridging of antibody fragments using compounds 33 and 34.

Fig l7:SDS-PAGE analysis shows that antibody fragments are sfully d by compounds 33 and 34.

WO 20151001117 5 Detailed ption of the invention The first object of the invention is a process for the labeling of a compound comprising a thiol moiety, comprising contacting said compound comprising a thiol moiety with a nd of formula (1) R4 wherein each of R1 to R5 is independently selected in the group consisting of: - hydrogen atoms, - alkyl, alkene or alkyne , optionally interrupted by at least one heteroatom selected among 0, N and S, 1 0 - aryl groups, - alkoxy groups, - halogen atoms, - amino (-NRR’) groups, wherein R and R’ are independently hydrogen atoms, alkyl, alkene, alkyne or aryl groups as defined below, - hydroxylamine (-ONH2) group, - hydrazine (-NH-NH2) group, - nitro (—N02) group, - azido (-N3) group, - diazoniurn (-N2+) group, optionally in presence of a counterion, - maleimide group, - alkyl- or aryl-carboxyl (-C(=O)OR) groups, wherein R is as described above, - alkyl- or aryl-carbonyl (-C(=O)R) groups, wherein R is as described above, - hydroxyl (-OH) group, - boronic acid -B(OR’ ’)2 group, wherein R’ ’ is a en atom or an alkyl group, - phosphine or phosphonium groups, - isocyanate O) or isothiocyanate (-N=C=S) group, - chlorosulfonyl (-SOzCl) group, - a O)-C(N2)-CF3 group or a -C(=O)—C(N2)_CF3 group, - activated esters, such as -C(=O)-NHS, wherein NHS stands for N- hydrosuccinimidyl, perfluorinated esters, and acylureas, WO 20151001117 6 2014/064387 - a -CEC-CEN group, - tags, and - alkyl groups tuted by at least one of the previously listed groups, wherein at least one of R1 to R5 comprises, preferably is, a tag moiety.

Two of R1 to R5 may alternatively form together and with the carbon atoms of the phenyl ring to which they are linked a mono or polycyclic ring, saturated, unsaturated or aromatic, optionally comprising at least one atom such as P, O or S.

The tag moiety that is comprised in the compound of formula (I) may be directly bonded to the phenyl ring. It may also be bonded to the phenyl ring h a “linker” group, such as a C00, a NH-C(=O)—NH, a NH-C(=O)—O, a triazole, or a CONH group.

It may also be present as a substituent of one of the R1 to R5 groups as described above.

In a preferred embodiment, R2, comprises, ably R3 is, a tag moiety.

In the present invention, the term “alkyl” relates to a linear, cyclic or branched hydrocarbon group comprising from 1 to 20 carbon atoms, preferably from 1 to 6 carbon atoms, in particular from 1 to 3 carbon atoms. Among alkyl groups can be cited for instance the , ethyl, n-propyl, isopropyl, n-butyl, sec—butyl, tert-butyl, n- pentyl, n-hexyl and cyclohexyl groups. An alkyl group according to the invention may be interrupted by at least one heteroatom selected from Si, N, O and S. Among alkyl groups interrupted by at least one heteroatom may be cited the polyethyleneglycol groups of formula -(OCH2-CH2)n-OH, wherein n is from 1 to 1000, preferably from 1 to 100, in particular from 1 to 8. An alkyl group according to the invention may be tuted by at least one halogen atom.

The term “alkene” relates to an alkyl group as defined above, further comprising at least one C=C double bond.

The term “alkyne” relates to an alkyl group as defined above, r comprising at least one CEC triple bond. Among alkyne groups can be cited for instance acetylene and cyclooctyne groups.

The term “alkoxy” relates to an alkyl group as defined above linked to the rest of the molecule via an oxygen atom.

WO 20151001117 7 The term “aryl” s to a group comprising at least one planar ring comprising a conjugated 7: system made of double bonds and/or non-bonding doublets, wherein each atom of the ring comprises a p orbital, the p orbitals overlay each other, and the delocalization of the n electrons lowers the molecule energy. Preferably, the aryl group is a hydrocarbon aryl group, optionally sing at least one heteroatom selected from N, O and S. Preferably, an aryl group is selected from the group consisting of phenyl, pyridinyl, pyrimidinyl, pyrazinyl, pyridazinyl, triazinyl, furanyl, thiophenyl, pyrrolyl, imidazolyl, thiazolyl, oxazolyl, isoxazolyl, dihydroisoxasolyl, triazolyl, diazinyl, tetrazinyl, pyrazolyl and naphthyl . In particular, an aryl group is selected from the group consisting of isoxazolyl, dihydroisoxasolyl, triazolyl, diazinyl, tetrazinyl and pyrazolyl groups.

The term “halogen” relates to an atom selected from the group ting of F, Cl, Br and I atoms. Preferably, a halogen is a C1 or Br atom.

The optical and rical isomers, racemates, tautomers, salts, hydrates, solvates and mixtures thereof of the compounds are also encompassed by the scope of formulas (I), (II), (III) and (IV) of the present invention.

When the nds according to the invention are in the forms of salts, they are preferably pharmaceutically able salts. Such salts include pharmaceutically acceptable acid addition salts, pharmaceutically acceptable base addition salts, pharmaceutically acceptable metal salts, um and ted ammonium salts.

Acid addition salts include salts of inorganic acids as well as organic acids. entative examples of suitable inorganic acids include hydrochloric, hydrobromic, odic, phosphoric, sulfuric, nitric acids and the like. Representative examples of le organic acids include formic, acetic, oroacetic, trifluoroacetic, propionic, benzoic, cinnamic, citric, fiamaric, glycolic, lactic, maleic, malic, malonic, mandelic, oxalic, , pyruVic, salicylic, succinic, methanesulfonic, ethanesulfonic, tartaric, ascorbic, pamoic, hylene salicylic, ethanedisulfonic, gluconic, citraconic, aspartic, stearic, palmitic, EDTA, glycolic, p—aminobenzoic, glutamic, benzenesulfonic, p-toluenesulfonic acids, sulphates, nitrates, phosphates, perchlorates, borates, acetates, benzoates, hydroxynaphthoates, glycerophosphates, ketoglutarates and the like. Further WO 20151001117 8 examples of pharmaceutically acceptable inorganic or organic acid addition salts include the pharmaceutically acceptable salts listed in J. Pharm. Sci. 1977, 66, 2.

Preferably, the salt does not comprise any thiol moiety.

The “counterion” can be any ion appropriate for compensating the charge of the diazonium group, and may be easily chosen by anyone of ordinary skill in the art. For instance, the counterion may be selected from the group consisting of halogenates, BF4', N03", HSO4‘, PF6' CH3COO', N(SOzCF3)2', CngOs', CH3803', CF3COO', (CH30)(H)P02' and N(CN)2'.

In the present invention, the yl (OH), amino (NH2 or NHR) and carboxyl (COOH) groups may be protected with appropriate protecting . One can refer to T. W. Green, P. G. M. Wuts, Protective Groups in Organic Synthesis, Wiley- Interscience, New York, 1999.

Among ting groups for hydroxyl groups may be cited acetyl (Ac), benzoyl (Bz), benzyl (Bn), B-Methoxyethoxymethyl ether (MEM), Dimethoxflrityl, [bis-(4- methoxyphenyl)phenylmethyl] (DMT), Methoxymethyl ether (MOM), Methoxytrityl [(4-methoxyphenyl)diphenylmethyl, MMT), p-Methoxybenzyl ether (PMB), Methylthiomethyl ether, Pivaloyl (PiV), Tetrahydropyganyl (THP), ydrofuran (THF), andm (triphenylmethyl, Tr).

Among protecting groups for amino groups may be cited t-butyl carbamate (Boc), 2- trimethylsilylethyl carbamate (Teoc), l—(l-Adamantyl)—l-methylethyl carbamate (Adpoc), l-Methyl-l-(4-biphenyl)ethyl carbamate (Bpoc), l-(3,5—Di-t—butylphenyl)-lmethylethyl carbamate (t—Bumeoc), l—Adamantyl Carbamate , p-Methoxybenzyl carbamate (Moz), 9-Anthrylmethyl carbamate, Diphenylmethyl Carbamate, 9- Fluorenylmethyl ate (Fmoc), ulfo) Fluoroenylmethyl carbamate, 9-(2,7- dibromo)Fluorenylmethyl ate, 2,7-Di-t-butyl-[9-(lO, lO-dioxo-lO,lO, 10,10- tetrahydrothioxanthyl)]methylcarbamate (DBD—Tmoc), 2-(N,N— dicyclohexylcarboxamido)ethlearbamate, 2-Phosphonioethyl carbamate (Peoc), 2- Phenylethyl carbamate, Benzyl carbamate (Cbz), Allyl ate (Alloc), l- Isopropylallyl carbamate (Ipaoc), 4-Nitrocinnamyl Carbamate (Noc), 8-Quinolyl carbamate and N—Phtalimide.

WO 20151001117 9 Among protecting groups for carboxyl groups may be cited methyl esters, benzyl esters, tert-butyl esters, silyl esters, 2,6-dimethylphenol, 2,6-diisopropylphenol, and 2,6-di-tert- butylphenol.

The term “tag” or “tag moiety” s to a chemical group appropriate for allowing one or several of the following: — detection of the nd, - vectorization of an agent of interest by the compound, - solubilization of the compound, - stabilization of the compound, - improvement of the extraction and/or purification of the compound, - modification of at least one of the ADME (Administration Distribution Metabolisation Excretion) parameters of the compound; - addition of bioactivity to the compound; - on of an appropriate functionality for click-chemistry.

The compounds comprising such tags and according to the invention can therefore be used as a tool for detection, vectorization of an agent of interest, solubilization, stabilization, ement of the extraction and/or purification, modification of at least one of the ADME (Administration Distribution lisation Excretion) parameters; addition of bioactivity; and/or addition of an appropriate fiinctionality for click- chemistry.

A chemical group appropriate for allowing detection of the compound of the invention may be any chemical group that can be identified and/or quantified by any technique of is known in the art. Among tags for detection can be cited fluorescent, such as cent probes, such as cein, quantum dots, cyanine dyes Cy3® and Cy5®, Alexa Fluor® dyes, t fluor® dyes, IRIS® Dyes, Seta® dyes, SeTau® dyes, ® dyes, Square® dyes, Nile red, iFLi[AMIJ or carboxytetramethylrhodamine (TAMRA); Nuclear Magnetic Resonance (NMR) tags, such as xenon or lanthanides (in particular terbium Tb or europium Eu); magnetic resonance imaging (MRI) contrast agents such as Gd chelates; mass spectrometry tags such as tris(2,4,6- WO 20151001117 10 trimethoxyphenyl)phosphonium (TMPP) or isotope-coded tags; infrared (IR) tags; positron emission tomography (PET) tags; single-photon on computed tomography (SPECT) tags; tritium or deuterium atoms; microscopy tags such as gold nanoparticles; quenchers such as dabsyl (dimethylaminoazobenzene sulfonic acid).

A chemical group appropriate for allowing vectorization of an agent of st with the compound of the invention may be any chemical group or biological moiety appropriate for helping the compound and/or the agent of interest to reach the riate tissue or organ, such as liver or bladder. For instance, the vectorization tag may be a chemical group able to form micelles, reverse-micelles or liposomes, such as an amphiphilic chemical group, a nano or article, a viral vector, a polymer, a folate, an ammonium group, a peptide, an EGFR (Epidermal Growth Factor Receptor) ligand or an dy.

A al group appropriate for allowing ization of the compound is a chemical group that affords increasing the half—life of the compound, preferably in viva. For instance, the stabilization tag may be n, such as Human Serum Albumin HSA or Bovine Serum Albumin BSA.

A chemical group appropriate for allowing ation of the ADME parameters of the compound can be for instance a eutic agent, a drug, a prodrug, a polyethylene glycol of a -(OCH2-CH2)n-OR”, wherein R” is a hydrogen atom or an alkyl group, wherein n is from 1 to 1000, preferably from 1 to 100, in particular from 1 to 8, a peptide, such as Proline-Alanine-Serine (Pro-Ala-Ser) or poly-Glu, a polypeptide, such as XTEN recombinant polypeptide, a lipid, such as palmitic acid, a carbohydrate, hydroxyethyl starch, a nucleic acid, such as DNA or RNA, in particular siRNA. The term “prodrug” relates to a variant of a drug that can be transformed in viva into a drug.

The term “peptide” relates to a peptide comprising from 1 to 20, preferably from 1 to , aminoacids.

The selection of the appropriate tag, such as the determination of the number of ethylene glycol moieties, can be easily adjusted by one of ordinary skill in the art depending of the desired ADME modification.

WO 20151001117 11 A chemical group appropriate for allowing tion and/or purification of the compound may be any chemical group that favors and/or facilitates the extraction and/or purification of the compound of the ion. Among extraction and/or purification-tags can be cited biotin, chelating tags such as DTPA (diethylenetriaminepentaacetic acid), EDTA (ethylenediamine-N,N,N',N'-tetraacetic acid), NTA (nitrilotriacetic acid) and D4 (octamethylcyclotetrasiloxane), protein tags such as polyarginine or polyhistidine tags, preferably His6 or Hile tags, FLAG-tag, Strep-tag, c-myc-tag, S-tag, calmodulin-binding e, cellulose-binding domain, g, chitin-binding domain, hione S-transferase tag, maltose-binding protein, NusA, TrxA and DsbA tags, boronic tags such as ospiro[isobenzofiiran-1(3H),9'- nthene]-3 ’,6’-diyl)bis(iminomethylene—2, l lene)]bis-(9Cl), perfluoroalkyl groups, ionic (cationic or anionic) groups, such as ammonium groups, and solid surfaces such as polymeric materials, in particular polyethylene beads, nanoparticles, in particular magnetic nanoparticles, chips, silica beads or silica wafers.

A chemical group appropriate for addition of bioactivity may be for instance a chemical group comprising at least one radioisotope, such as 131I, 90Y, 89Sr, or 153Sm, or a derivative thereof.

A chemical group appropriate for reacting in click-chemistry may be for instance a chemical group selected from the group consisting of azides (such as N3) and strained alkynes, in particular cyclic alkynes. Among cyclic alkynes may be cited for instance the bicyclononyne (BCN) and tetramethylthiepinium (TMTI) moieties.

In an embodiment, each of R1 to R5 is independently selected in the group ting of: - alkyne , - amino groups, - hydroxylamine (-ONH2) groups, - hydrazine (-NH-NH2) groups, - azido (N3) groups, - diazonium (Nf) groups, preferably in presence of a counterion, - maleimide groups, wo 2015;001117 12 - carboxylic acid , - aldehyde (-CHO) groups, - c -B(OR’ ’)2 groups, wherein R” is as described above, and - activated esters.

In a preferred embodiment, none of R1 to R5 comprises a free SH group. In a preferred ment, R1 and/or R5 do not comprise any nucleophilic group, such as amino groups, hydroxylamine groups, hydrazine groups or hydroxyl groups.

In specific embodiments, l, 2, 3, 4 or 5 of R1 to R5 are different from hydrogen atoms.

In specific embodiments, at least one of R1 to R5 comprises at least one moiety that is appropriate for further forming a covalent bond with a chemical group selected in the group consisting of thiol (SH) moieties, amine (NHz) moieties and carboxylic acid (COOH) es. Among moieties appropriate for forming a covalent bond with thiol es, one can cite maleimide moieties. Among moieties appropriate for forming a covalent bond with amine moieties, one can cite NHS-ester moieties.

Among compounds of formula (I) ing to the present invention may be cited the following compounds: N N N N || || || || || || || H H H N‘Boc NH2 NH2 N‘Boc o o o o HO o HO o + + 36 68 69 70 W0 01117 13 HN Q fill El 46: \\ W0 01117 14 TFA‘ \ \0 0’ o 55 / g?:5 0/ /O 0/ HN 0 73 40 INI N Q INI _N+_ I H —~+— II IN H o m) 0 O O O O 1:1F F F FmocHN F F F O OH 76 SO3Na 77 78 18': CF218F 125' 79 so 81 82 WO 20151001117 15 ° and N%©~N\\ /_/_SO3H N N Among compounds of formula (I) may also be cited the ing compounds: N 20 W0 01117 O NH o o I I \/\o I/N 0 OH N \\ / N WO 20151001117 17 2014/064387 O OH N: : N\’MONOV\ONO\/\o/\)LNH O OH 0%HN ”NOWONOWONOWONOWNHZ fi0 51 WO 20151001117 18 o\\\ HN 0 N/N:N N: : Wowo~°v\o/\/°j // m , ’N / / 0 N / JL N" N \N/\/\N F I H H F F 53 01‘ 63 Synthesis of comgonnds 0f the invention Compounds of formula (I) or (II) according to the invention can be synthesized for instance in two steps from the corresponding iodoarene, by coupling with propargyl alcohol, for instance Via a shira coupling. The coupling is preferably followed by oxidation; for instance, the oxidation may be a tandem oxidation performed with Mn02 in the presence of an ammonia solution. Alternatively, the compounds of the invention can be sized by cyanation of arylalkynes. Cyanation may be performed for ce with CuCN, arylisocyanates, cyanobenzotriazoles or cyanoimidazoles. [fibeling 0t comgonnds sing at least one thiol moiety The compounds of formula (I) may be used in a process for labeling compounds comprising at least one thiol SH moiety. Preferably, the process of the invention comprises contacting at least one nd of formula (I) with a compound comprising at least one thiol SH , or a sample susceptible to comprise such a compound. ably, the sample is a biological sample, in particular an aqueous sample.

WO 20151001117 19 The term “labeling” in the present invention refers to the formation of a covalent bond between the sulfur atom of the thiol moiety and the lonitrile moiety of the nds of formula (I).

The compound comprising a thiol moiety (R6-SH nd) can be for ce a fluorophore, a quencher, an amino acid, a peptide, a protein, an enzyme, a drug, a prodrug and/or a drug metabolite.

R6 may be any chemical group that is bonded to a thiol (SH) group to form a “compound comprising a thiol moiety”. R6 preferably comprises carbon, hydrogen, oxygen, nitrogen, phosphorus, and/or sulphur atoms.

In particular, the nd comprising a thiol moiety can be cystein, or a derivative, such as an ester, thereof, or a e or a protein comprising at least one cystein residue. Alternatively, the compound sing a thiol moiety may be a surface presenting at least one free SH group.

Labeling of the compounds comprising a thiol moiety with compounds of formula (I) may be used for a great number of applications.

In a first embodiment, labeling of the nds comprising a thiol moiety with nds of formula (I) may be used in the detection and/or fication of the compound comprising the thiol moiety in a sample. The detection means in the present invention fying the presence or absence of the desired compound(s) in the sample.

The sample can be any sample susceptible to comprise the compound comprising at least one thiol moiety. For instance, the sample may be a biological sample, for instance a biological fluid, such as blood, plasma, serum, saliva, urine, etc., an extract of natural products, a biological tissue, or a part thereof, or a medium comprising cells.

In a second embodiment, labeling of the compounds comprising a thiol moiety with compounds of formula (I) may be used for conjugation of the compound comprising a thiol moiety with a moiety that improves its physico-chemical properties. For instance, the conjugated moiety may improve the solubility of the compound comprising a thiol moiety, or improve its synthesis and/or purification.

WO 20151001117 20 In a third embodiment, labeling of the compounds sing a thiol moiety with compounds of a (I) may be used for bio-conjugation of the compound sing a thiol moiety with a compound of interest, such as a drug, a prodrug, a carbohydrate or a protein.

For ce, a compound of formula (1) comprising a compound of interest as tag may allow selective vectorization and/or binding of the compound of interest to the compound comprising at least one thiol moiety.

Another object of the invention is a nd of formula (I) as defined above, including the described specific embodiments.

The invention also discloses a compound of formula (11) R4 R5 wherein each of R1 to R5 is selected independently in the group consisting of: - hydrogen atoms, - alkyl, alkene or alkyne groups, optionally upted by at least one heteroatom selected among 0, N and S, - aryl groups, - alkoxy groups, - halogen atoms, - amino (-NRR’) groups, wherein R and R’ are independently en atoms or alkyl, alkene, alkyne or aryl groups as defined above, - hydroxylamine (-ONH2) group, - hydrazine (-NH-NH2) group, - nitro (-N02) group, - azido (—N3) group, - diazonium (-N2+) group, preferably in presence of a counterion, - rnaleimide group, WO 20151001117 21 - alkyl- or aryl-carboxyl (—C(=O)OR) groups, - alkyl- or aryl-carbonyl (-C(=O)R) groups, - hydroxyl (-OH) group, - boronic -B(OR’ ’)2 group, wherein R” is a hydrogen atom or an alkyl group, - phosphine or phosphonium groups, - isocyanate (-N=C=O) or isothiocyanate (-N=C=S) group, - chlorosulfonyl (-SOzCl) group, - a O-C(=O)-C(N2)-CF3 group or a -C(=O)-C(N2)_CF3 group, - activated esters, such as -C(=O)-NHS, perfluorinated esters and acylureas, lO - tags, and - alkyl groups tuted by at least one of the previously listed groups.

The compounds of formula (II) are linkers to which at least one tag may be added to form the compounds of formula (I) as bed above.

Among the compounds of a (11) according to the t invention may be cited the following compounds: N N | | | | || || Né Ne c\\S CQO 21 84 WO 1117 22 SE [NI l 1 I”I H | | ‘ ‘ 0 NH 0 NH N SO3Na OH 0 N \ o o / 0 O HO U 89 90 41 N INI H N H INI H INI || ” H H " J, a T T NHMe NHAc WO 2015001117 23 2014/064387 | | N I I 'N' I I II II II n | | || M NO; OMe NHAc 93 1 I I II II N I I I I I I COO” NH2 \\ INI 7 1s 34 \N 35 or 3 Among the compounds of formula (11) according to the present invention may also be cited the following compounds: //N //N & ¢ ¢ | F3C O 13 14 15 5L )1 X N N/\/\O/\/O\/\O/\/\N O H H H WO 2015001117 24 H H O \/\o/\/O\/\/N\n/Oj<O / N N \ / N //N / \ / % é / o O/ /\OJJ\N 0‘ H 0 26 31 32 YNH H 0 HN ‘\\\MNNO%ONN H S 0 o NH I I ‘N:N 42 61 WO 20151001117 25 HN O F38k0.

O b; O s\ ”V 8 IN _ _N O' ll N\N F M NH; 62 64 65 The s for labeling a compound comprising a thiol moiety according to the invention may further comprise, before the step of contacting the compound comprising a thiol moiety With a compound of formula (I), a preliminary step of preparation of the compound of formula (1), comprising contacting a compound of formula (II) with a compound sing a tag moiety, or a sor thereof.

The term “precursor” relates in the present case to a chemical group that is able to form, after contacting with the compound of a (II), the tag moiety.

Preferably, at least one of R1 to R5 is different from a hydrogen atom.

An object of the invention is a compound of formula (11), wherein at least one of R1 to R5 comprises, preferably is, a maleimide, an azide (N3) group, an alkyne or a NHS-ester moiety.

W0 20151001117 26 The maleimide and NHS-ester moieties respectively allow fiarther g of the compound to another thiol or an amine group; the N3 group allows further linking of the compound to another alkyne—group and the alkyne group allows further linking of the compound to another N3 group.

In an embodiment, the compound of formula (11) according to the ion is selected from the following compounds: N N N l | l | | | N N || || || II N HN O HN 0 O O l é) || || 71 —SI— N _ | //N+ 29 3O 19 WO 20151001117 27 The invention also s to compounds of formula (I) or (11), wherein at least one of R1 to R5 is further bonded to a compound of interest.

A compound of interest may be for instance a le, such as a fluorophore, for instance rhodamine, a group of atoms comprising at least one radioactive atom (14C, 3H, or 131I for instance), a group of atoms of known mass (a mass tag), a ligand, a drug, a therapeutic agent, a biomolecule, such as an antibody, a protein, such as BSA (bovine serum albumin), a DNA fragment, a nanoobject, such as a nanoparticle (ie an object or a particle of 0.1 to 1000 nm), or a support, such as a polymer.

When the process of labeling according to the ion is performed with such a compound of formula (I) or (11) wherein at least one of R1 to R5 is further bonded to a compound of interest, the process affords the formation of a conjugate between the compound of interest and the compound comprising a thiol .

In an embodiment, the compound of interest is a biomolecule such as a n or an antibody, and the compound comprising a thiol moiety is a fluorophore such as a compound comprising a TAMRA moiety and a thiol moiety (TAMRA-SH).

In an embodiment, the compound of interest is a biomolecule such as a protein or an antibody, and the compound sing a thiol moiety is a drug or a therapeutic agent.

The conjugate obtained by the process of labeling according to the invention is a therapeutic dy.

Another object of the invention is a compound of formula (111): R2 R1 S_R6 R4 R5 /// (HI) , n R6-S corresponds to the moiety of the compound comprising at least one thiol moiety as defined above. In particular, the nd of formula (III) is of formula (IV): WO 20151001117 28 2014/064387 (1V) wherein R7 and Rs are selected in the group consisting of OH, tag, alkyl, O—alkyl, and peptidic moieties, wherein the alkyl groups may be substituted by at least one tag moiety. A peptidic moiety is a moiety comprising at least one aminoacid, when the moiety preents more than one aminoacid (2, 3, 4, 5, ...), the aminoacids are linked between each other by peptidic bonds. ably, the double bond of the compound of formula (III) or (IV) is of (Z) configuration. The tag and alkyl groups are as defined above.

Among compounds of formula (111) according to the present invention may be cited the ing compounds: TFA' 8+ I l \ / The compounds of formula (I) have surprisingly been found to be more stable in aqueous medium than the corresponding compounds wherein the 3—arylpropiolonitrile moiety is replaced with a maleimide moiety, which is classically used for ng thiol moieties. For instance, compound 1 E: was imately 25% hydrolyzed after 1h in buffer solution (kobs=7x10'5s'1), while no hydrolysis could be detected for WO 20151001117 29 ACN : :N nd 11 . Interestingly, even after a week at room temperature, no trace of hydrolyzed product could be detected for compound 11.

In addition, the compounds of formula (II) according to the invention showed a marked selectivity towards cysteine compared to other amino-acids which do not comprise free thiol es. Comparatively, the chemoselectivity obtained for the corresponding compounds wherein the 3-arylpropiolonitrile moiety is replaced with a maleimide moiety is lower.

Finally, the compounds of formula (III) as described above have shown to be highly more stable in biological conditions than the corresponding compounds wherein the 3- arylpropiolonitrile moiety is replaced with a maleimide moiety. For instance, the T/ CN on product NHBn between compound %c~ and cysteine H2Nle/NHBn derivative 3 0 was particularly stable in a wide range of conditions, such as physiological ions. In particular, said addition product was stable in a wide range of pH (from 0 to 14), and no exchange product could be observed after one hour of reaction with an excess of phenylthiol and glutathione.

The ion will be illustrated in more detail with reference to the following es, but it should be understood that the present invention is not deemed to be limited thereto.

WO 20151001117 30 2014/064387 Examples Example 1: Synthesis of compounds of the ion > S thesis of com ounds of formula II A series of compounds of formula (I) or (II) were synthesized and characterized according to the following procedures.

General protocols: Sonogashira coupling Standard reaction protocols: A. To a d on of the proper aryl halide (1 eq., 1 mmol) in DMF (5 mL) and DIPEA (10 eq., 10 mmol), premixed PdC12(PPh3)2 (0.03 eq., 30 umol) and CuI (0.06 eq., 60 umol) were added. Obtained reaction mass was degased, stirred for another 5 minutes, followed by the addition of propargyl l (1.2 eq., 1.2 mmol). The reaction mass was stirred for 1-24 hours (monitored by TLC). 1M HCl (50 mL) was added (if contains free amino , 50 mL of water were added instead) and the reaction mixture was extracted with ethyl acetate (3x20 mL). United ethyl acetate fractions were washed with water (1x10 mL) dried over MgSO4 and evaporated to give crude product.

Products were purified by flash chromatography (gradient of 20 minutes from 100% of cyclohexane to 100% of ethyl acetate).

B. To a degased solution of the proper aryl halide (1 eq., 1 mmol) in THF (5 mL) and TEA (5 mL), ed PdC12(PPh3)2 (0.03 eq., 30 umol) and Cu] (0.06 eq., 60 umol) were added, followed by the addition of propargyl alcohol (2 eq., 1.2 mmol). The reaction mass was stirred for 1-24 hours ored by TLC). THF and TEA were evaporated and the crude product was purified by flash chromatography (gradient of 20 minutes from 100% of cyclohexane to 100% of ethyl acetate).

C. To a degased solution of the proper aryl halide (1 eq., 1 mmol) in propylamine or pyrrolidine (3 mL), Pd(PPh3)4 (0.05 eq., 50 umol) was added. The reaction mass was heated overnight (30-50 °C), evaporated and the crude product was purified by flash chromatography (gradient of 20 minutes from 100% of cyclohexane to 100% of ethyl acetate).

WO 20151001117 31 Preparation of highly active MnOz A on of MnC12'4H20 (1 eq., 1 mole, 200 g) in water (2 L) at 70 0C was gradually added during 10 s, with stirring, to a solution of KMnO4 (1 eq., 1 mole, 160 g) in water (2 L) at 60 °C in a hood. A vigorous reaction ensued with ion of chlorine; the suspension was stirred for 2 hours and kept overnight at room temperature. The precipitate was filtered off, washed thoroughly with water (4 L) until pH 6.5-7 and the washing gave a negligible chloride test. The filter cake was then dried at 120—130 °C for 18 h; this gave a chocolate-brown, highly disperse amorphous powder.

MnOz oxidation OH R1 / R2 // Slightly modified procedure described by McAllister 824 To et al. a solution of the proper propargylic alcohol (1 eq., 1 mmol) in THF (4.5 mL), MgSO4 (15 eq., 15 mmol), highly active Mn02 (25 eq., 25 mmol) and 2M NHs solution in IPA (4 eq., 4 mmol, 2 mL) were added. Obtained reaction mass was vigorously stirred at room temperature for 05-12 hours (monitored by TLC). DCM (20 mL) were added and the obtained reaction mass was filtered h Celite, evaporated to give crude t and purified by flash chromatography if required.

WO 2015001117 32 Substituted 3-(aryl)propynols (la-12a): R3 R4 R3 R4 1a-12a R1 R2 R3 R4 X Protocol 1a OMe H H H I B 2a H OMe H H Br C 3a H H OMe H I B 4a OMe H H OMe I C 5a NH2 H H H I B 6a H NH2 H H I A 7a H H NH2 H I A 8a Me H H H I B 9a Me H H Me I A 10a N02 H H H Br B 11a H H NHAc H I A 12a H H CONHMe H I A 3-(2-Methoxyphenyl)propyn-l-ol (la).

Reaction time: 18 hours; yield: 72%. 1H NMR (400 MHz, OL-d4) 8 7.36 (dd, J = 1.5, 7.5 Hz, 1H), 7.26-7.33 (m, 1H), 6.97 (d, J = 8.3 Hz, 1H), 6.86-6.93 (m, 1H), 4.43 (s, 2H), 3.84 (s, 3H); 13C NMR (101 MHz, METHANOL-d4) 5161.6, 134.5, 131.0, 121.5, 113.4, 112.0, 92.7, 82.0, 56.2, 51.5. 3-(3-Methoxyphenyl)propynol (23). on time: 16 hours; yield: 87%. 1H NMR (400 MHz, METHANOL-d4) 5 7.15-7.24 (pseudo-t, J = 7.5 Hz, 1H), 7.00 (d, J = 7.5 Hz, 1H), 6.93-6.98 (m, 1H), 6.87 (dd, J: 2.13, 7.5 Hz, 1H), 4.41 (s, 2H), 3.73 (s, 3H); 13C NMR (101 MHz, METHANOL-d4) 5 160.9, 130.6, 125.4, 125.1, 117.8, 115.7, 88.8, 85.6, 55.9, 51.4. 3-(4-Methoxyphenyl)propynol (33).

Reaction time: 16 hours; yield: 92%.

WO 2015001117 33 1H NMR (400 MHz, CHLOROFORM-d) 8 7.40 (d, J = 8.78 Hz, 2H), 6.86 (d, J = 8.78 Hz, 2H), 4.51 (d, J: 4.9 Hz, 2H), 3.83 (s, 3H), 1.78 (t, J: 4.9 Hz, 1H); 13C NMR (101 MHz,CHLOROFORM-d)8159.8, 133.2, 114.6, 114.0, 85.9, 85.7, 55.3, 51.7. 3-(2-Aminophenyl)propynol (43).

Reaction time: 24 hours; yield: 62%. 1H NMR (400 MHz, METHANOL-d4) 8 7.19 (dd, J = 1.25, 7.9 Hz, 1H), 7.03-7.12 (m, 1H), 6.75 (d, J = 7.9 Hz, 1H), 6.56-6.65 (m, 1H), 4.47 (s, 2H), 4.26 (s, 2H); 13C NMR (101 MHz, OL-d4) 8 150.3, 133.0, 130.6, 118.2, 115.6, 93.8, 78.9, 69.5, 51.0. 3-(3-Aminophenyl)propyn-l-ol (53).

Reaction time: 18 hours; yield: 77%. 1H NMR (400 MHz, CHLOROFORM-d) 8 7.08 (t, J= 7.8 Hz, 1H), 6.83 (d, J = 7.8 Hz, 1H), 6.76 (s, 1H), 6.64 (dd, J = 1.5, 7.8 Hz, 1H), 4.46 (s, 2H), 2.17 (s, 1H); 13C NMR (101 MHz, FORM-d) 8 146.3, 129.2, 123.4, 122.0, 118.0, 115.5, 87.0, 85.6, 51.4. 3-(4-Aminophenyl)propyn01 (63).

Reaction time: 18 hours; yield: 42%. 1H NMR (400 MHz, METHANOL-d4) 8 7.11-7.21 (d, J: 8.5 Hz, 2H), 6.53-6.68 (d, J: 8.5 Hz, 2H), 4.37 (s, 2H); 13C NMR (101 MHz, METHANOL-d4) 8 149.7, 133.8, 115.7, 112.5, 86.7, 85.9, 51.4; 3-(2-Nitrophenyl)propynol (73). on time: 15 hours; yield: 35%. 1H NMR (400 MHz, CHLOROFORM-d) 8 7.97 (d, J = 8.0 Hz, 1H), 7.54—7.60 (d, J = 8.0 Hz, 1H), 7.46-7.54 (t, J = 8.0 Hz, 1H), 7.36-7.44 (t, J = 8.0 Hz, 1H), 4.49 (s, 2H), 1.68 (br. s., 1H); 13C NMR (101 MHz, CHLOROFORM-d) 8 149.9, 134.8, 132.8, 128.9, 124.6, 118.0, 95.2, 80.9, 51.7. 4-(3-Hydroxypropynyl)-N-methylbenzamide (83).

Reaction time: 12 hours; yield: 91%. 1H NMR (400 MHz, METHANOL-d4) 8 7.72-7.82 (m, J = 8.28 Hz, 2H), 7.41-7.53 (m, J = 8.28 Hz, 2H), 4.43 (s, 2H), 2.92 (s, 3H); 13C NMR (101 MHz, METHANOL—d4) 8 169.9,135.2,132.7, 128.3, 127.6, 91.5, 84.7, 51.3, 27.1.

N-(4-(3-Hydroxypropynyl)phenyl)acetamide (93).

Reaction time: 18 hours; yield: 85%.

WO 2015001117 34 1H NMR (400 MHz, METHANOL-d4) 8 7.56-7.64 (d, J = 8.8 Hz, 2H), 7.47-7.56 (d, J = 8.8 Hz, 2H), 4.74 (s, 2H), 2.04 (s, 3H); 13C NMR (101 MHz, METHANOL-d4) 8 171.9, 143.8, 135.7, 120.7, 112.8, 106.2, 84.5, 62.7, 24.1. 3-(0-Tolyl)propynol (1021).

Reaction time: 5 hours; yield: 70%. 1H NMR (400 MHz, CHLOROFORM-d) 6 7.40 (d, J = 7.5 Hz, 1H), 7.11-7.24 (m, 3H), 4.54 (s, 2H), 2.43 (s., 3H); 13C NMR (101 MHz, CHLOROFORM-d) 8 138.2, 131.2, 128.4, 128.0, 119.3, 115.3, 86.5, 85.2, 51.2, 21.2. 3-(2,6-Dimethylphenyl)propynol (lla).

Reaction time: 24 hours; yield: 25%. 1H NMR (400 MHz, CHLOROFORM-d) 8 7.03 (t, J= 7.5 Hz, 1H), 6.95 (d, J = 7.5 Hz, 2H), 4.50 (s, 2H), 2.34 (s, 7H); 13C NMR (101 MHz, CHLOROFORM—d) 8 140.5, 127.9, 126.7, 122.3, 95.6, 83.3, 51.9, 21.1. 3-(2,6-Dimethoxyphenyl)propynol (12a).

Reaction conditions: 30 °C, propylanline, 16 hours; yield: 38%. 1H NMR (400 MHz, OL-d4) 8 7.25 (t, J = 8.4 Hz, 1H), 6.62 (d, J = 8.4 Hz, 2H), 4.46 (s, 2H), 3.84 (s, 6H); 13C NMR (101 MHz, METHANOL—d4) 8 163.0, 131.0, 104.7, 102.5, 97.0, 78.1, 56.4, 51.7.

WO 20151001117 35 tuted 3-aryl-pr0piolonitriles (1-12): R, R1 / R2 // MnOZY Mgso4 R2 // NH3 (IPA), THF R3 R4 R3 R4 R1 R2 R3 R4 Time, h Yield, 0/0 1 OMe H H 3 45 2 H OMe H 2 85 3 H OMe H 3 95 4 OMe H H OMe 4 60 NH2 H H 1 47 6 H NH2 H 2 71 7 H H NH2 9 94 8 Me H H 1.5 70 9 Me H H Me 2 55 N02 H H H 4 21 11 H H NHAC H 2 92 12 H H CONHMe H 2 61 3-(2-Methoxyphenyl)pr0piolonitrile (1, APN-o-OMe). 1H NMR (400 MHz, METHANOL-d4) 8 7.51-7.65 (m, 2H), 7.12 (d, J = 8.3 Hz, 1H), 7.01 (t, J = 7.7 Hz, 1H), 3.94 (s, 4H); 13C NMR (101 MHz, METHANOL—d4) 8 164.7, 136.4, 135.3, 122.0, 112.6, 107.7, 106.4, 81.8, 66.7, 56.7; IR (neat film, cm'l): 2946, 2264, 2142 1596, 1490, 1245, 1164, 1122, 1047, 1021, 752, 498; GC-ESI-HRMS: 157.05276; found 157.05044. 3-(3-Methoxyphenyl)pr0piolonitrile (2, APN-m-OMe). 1H NMR (400 MHz, METHANOL-d4) 8 7.38 (t, J = 7.8 Hz, 1H), 7.27 (d, J = 7.8 Hz, 1H), 7.20-7.24 (m, 1H), .20 (m, 1H), 3.83 (s, 3H); 13C NMR (101 MHz, METHANOL—d4) 8 161.2, 131.4, 127.1, 120.0, 119.4, 119.2, 106.0, 84.1, 62.7, 56.1; IR (neat film, cm‘l): 2491, 2264, 2144, 1595, 1573, 1488, 1464, 1420, 1324, 1294, 1207, 1178, 1045, 783, 681, 494; GC-ESI-HRMS: 157.05276; found 157.05298. 3-(4-Methoxyphenyl)pr0piolonitrile (3, APN-p-OMe). wo 2015;001117 36 1H NMR (400 MHz, CHLOROFORM-d) 8 0 (m, J = 8. 8 Hz, 2H), 6.86-6.96 (m, J = 8.8 Hz, 2H), 3.86 (s, 3H); 13C NMR (101 MHz, CHLOROFORM-d) 8 161.4, 134.4, 113.7, 108.2, 104.8, 82.7, 61.5, 54.5; IR (neat film, cm'l): 2985, 2358, 2342, 2263, 2178, 2149, 1603, 1514, 1307, 1270, 1180, 1028, 835, 808, 669, 424; GC-ESI- HRMS: 157.05276; found 157.05337. 3-(2,6-Dimethoxyphenyl)propiolonitrile (4, AFN-0,0 ’-diOMe): 1H NMR (400 MHz, CHLOROFORM—d) 8 7.38 (t, J: 8.5 Hz, 1H), 6.53 (d, J = 8.5 Hz, 2H), 3.88 (s, 6H); 13C NMR (101 MHz, CHLOROFORM-d) 8 164.4, 133.8, 106.2, 103.4, 96.5, 77.7, 70.5, 562; IR (neat film, cm'l): 2847, 2359, 2259, 2201, 2139, 1926, 1586, 1574, 1478, 1432, 1302, 1255, 1188, 1109, 1025, 778, 727, 648, 632, 545, 506, 488, 420; GC-ESI-HRMS: 187.06333; found 184.06465. 3-(2-Aminophenyl)propiolonitrile (5, APN-o-NHz). 1H NMR (500 MHz, METHANOL-d4) 8 6.81 (d, J = 7.88 Hz, 1H), 6.65-6.76 (m, 1H), 6.08-6.19 (m, 2H), 3.85 (br. s., 1H); 13C NMR (126 MHz, CHLOROFORM-d) 8 151.4, 134.0, 133.4, 118.2, 115.0, 105.8, 101.0, 81.6, 68.5; IR (neat film, cm'l): 3413, 3332, 3211,2925, 2853,2250, 2136, 1632, 1600, 1563, 1486, 1452, 1312, 1273, 1252, 1161, 740, 673, 493; GC-ESI-HRMS: 142.05310; found 142.05458. 3-(3-Aminophenyl)propiolonitrile (6, APN-m-NHz). 1H NMR (400 MHz, CHLOROFORM-d) 8 7.17 (t, J: 7.6 Hz, 1H), 6.99 (d, J = 7.6 Hz, 1H), 6.74-6.89 (m, 2H), 3.85 (br. s., 2H); 13C NMR (101 MHz, CHLOROFORM-d) 5 146.8, 129.8, 123.6, 118.7, 118.7, 118.0, 105.7, 83.7, 623; IR (neat film, cm'l): 3426, 3340, 2923, 2852, 2265, 2142, 1630, 1594, 1579, 1513, 1448, 1326, 1313, 1300, 1220, 1164, 993, 882, 862, 784, 680, 534, 456; -HRMS: 142.05310; found 142.05197. 3-(4-Aminophenyl)propiolonitrile (7, APN-p-NHz). 1H NMR (400 MHz, METHANOL-d4) 5 7.26 (d, J = 8.6 Hz, 2H), 6.51 (d, J = 8.6 Hz, 2H); 13C NMR (101 MHz, METHANOL-d4) 8 152.5, 135.1, 113.6, 105.6, 102.3, 86.3, 60.2; IR (neat film, cm‘l): 3431, 3333, 3211,2250, 2132, 1632, 1599, 1513, 1438, 1303, 1178, 1043, 949, 826, 814, 526, 495, 452; GC-ESI-HRMS: 142.05310; found 142.05464. 3-(0-Tolyl)propiolonitrile (8, APN-o-Me). 1H NMR (400 MHz, FORM-d) 8 7.47 (d, J = 7.78 Hz, 1H), 7.28-7.36 (m, 1H), 7.18 (d, J = 8.03 Hz, 1H), 7.08-7.16 (m, 1H), 2.39 (s, 3H); 13C NMR (101 MHz, W0 20151001117 37 CHLOROFORM-d) 8 143.4, 134.1, 131.8, 130.1, 126.1, 117.4, 105.6, 82.4, 66.4, 20.5; IR (neat film, cm'l): 2295, 2257, 2141, 1599, 1484, 1456, 1383, 1291, 1199, 1162, 1116, 1039, 757, 711, 672, 548, 490, 452; GC-ESI-HRMS: 141.05785; found 141.05926. 3-(2,6-Dimethylphenyl)propiolonitrile (9, APN-o,0’-diMe). 1H NMR (400 MHz, CHLOROFORM-d) 8 7.12-7.27 (t, J = 7.5 Hz, 1H), 7.01 (d, J = 7.5 Hz, 2H), 2.38 (s, 6H); 13C NMR (101 MHz, CHLOROFORM-d) 8 143.8, 131.2, 127.3, 117.6, 105.6, 81.5, 70.2, 20.8; IR (neat film, cm'l): 2923, 2856, 2261, 2138, 1732, 1595, 1468, 1381, 1265, 1168, 1033, 774, 728, 490; GC-ESI-HRMS: 15507350; found 507. 3-(2-Nitrophenyl)propiolonitrile (10, APN-o-NOz). 1H NMR (400 MHz, METHANOL-d4) 8 8.28 — 8.35 (m, 1H), 7.96 — 8.06 (m, 1H), 7.81 — 7.90 (m, 2H); 13C NMR (101 MHz, METHANOL-d4) 8 151.9, 138.3, 135.2, 134.1, 126.6, 114.2, 105.7, 79.0, 68.6; IR (neat film, cm‘l): 2268, 1604, 1567, 1528, 1502, 1480, 1345, 851, 787, 744, 709, 687, 537, 491; GC-ESI-HRMS: 172.02728; found 172.02869.

N-(4-(Cyanoethynyl)phenyl)acetamide (11, APN-p-NHAc). 1H NMR (400 MHz, METHANOL—d4) 5 .63 (m, J = 8.8 Hz, 2H), 7.49-7.56 (m, J = 8.8 Hz, 2H), 2.04 (s, 3H); 13C NMR (101 MHz, METHANOL—d4) 8 171.9, 143.8, 135.7, 120.7, 112.8, 106.2, 84.5, 62.7, 24.1; IR (neat film, cm‘l): 3303, 3174, 3098, 2278, 2262, 2139, 1670, 1594, 1535, 1407, 1364, 1321, 1263, 1177, 834, 534; GC-ESI- HRMS: 184.06366; found 184.06212. 4-(Cyanoethynyl)-N-methylbenzamide (12, APN-p-CONHMe): 1H NMR (400 MHz, METHANOL-d4) 8 .05 (m, J = 7.78 Hz, 2H), 7.85-7.93 (m, J = 7.78 Hz, 2H), 3.03 (s, 3H); 13C NMR (101 MHz, METHANOL-d4) 8 169.1, 138.3, 134.9, 129.0, 121.6, 105.9, 83.0, 64.6, 28.8; IR (neat film, cm'l): 3348, 2270, 1641, 1549, 1502, 1408, 1392, 1327, 1303, 1283, 1162, 854, 760, 617, 488; GC-ESI-HRMS: 184.06366; found 184.06465.

WO 20151001117 38 2014/064387 3-(4-10d0phenyl)propiolonitrile (13): é OH / MnOz, Mgso4 é NH3/IPA/THF | r.t., 2h I Product was synthesized according to general procedure of MnOz-oxidation. Reaction time: 30 minutes; yield: 61%. 1H NMR z, CHLOROFORM-d) 8 = 7.78 (d, J = 8.5 Hz, 2H), 7.32 (d, J = 8.5 Hz, 3H); 13C NMR (101 MHz, chloroform-d) 8 138.1, 134.4, 116.8, 105.2, 99.2, 81.9, 64.2.

Compound 13 can be used for the labeling method according to the invention (with radioisotope 1251). 3-(4-(Triflu0r0methyl)phenyl)pr0piolonitrile (14): é OH / Mn02,MgSO4 é NH3/IPNTHF F3C r.t.,2h F3C Product was synthesized according to general procedure of MnOz-oxidation. Reaction time: 1 hour; yield: 45%. 1H NMR (400MHz, CHLOROFORM-d) 5 = 7.76 (d, J = 8.3 Hz, 2H), 7.70 (d, J = 8.3 Hz, 2H).

Compound 14 can be used for the labeling method according to the invention (with radioisotope 18F). tert-Butyl 4-(3-hydr0xypr0pynyl)benz0ate (15a): Refri— XorC/OH Product was synthesized according to general procedure B for coupling. Yield : 98%.

WO 2015001117 39 1H NMR (400MHz, CHLOROFORM-d) 5 = 7.93 (d, J = 8.1 Hz, 2H), 7.47 (d, J = 8.1 Hz, 2H), 4.53 (s, 2H), 1.60 (s, 9H); 13C NMR (101MHz, CHLOROFORM-d) 5 = 165.1, 131.7, 131.4, 129.3, 126.6, 89.8, 85.1, 81.4, 51.6, 28.1. utyl 4-(cyanoethynyl)benz0ate (15): / // / Mno2 Mgso4 ¢ NH3/IPtA/THF X0 Product was synthesized according to l procedure of MnOz-oxidation. Reaction time: 15 minutes; yield: 48%. 1H NMR (400MHz, DMSO-ds) 5 = 8.00 (d, J = 8.3 Hz, 2H), 7.94 (d, J = 8.3 Hz, 2H), 1.56 (s, 9H); 13C NMR (101MHz, CHLOROFORM-d) 5 = 164.3, 134.8, 133.3, 129.7, 121.3, 105.2, 82.2, 81.9, 64.8, 28.1. 4-(Cyanoethynyl)benz0ic acid (16): //N //N ¢ ¢ X0 ’ o 0 To the solution of tert-butyl 4-(2-cyanoeth—I-yn-I—yl)benz0ate (1 eq., 350 mg, 1.54 mmol) in MeCN (14 mL) was added TFA (30.6 eq., 5.372 g, 3.5 mL, 47.1 mmol) . The mixture was stirred for 36h at r.t. and then d and washed with 3X2 mL of EtzO.

The precipitate consisted of pure 4-(2-cyanoeth-I-yn-I-yl)benz0ic acid (140 mg, 0.823 mmol, 53% yield). 1H NMR (400MHz, METHANOL-d4) 8 = 8.12 (d, J = 8.3 Hz, 3H), 7.83 (d, J = 8.3 Hz, 2H).

Perfluorophenyl 4-(cyan0ethynyl)benz0ate (1 7): WO 01117 40 16 17 The solution of pentafluorophenol (1 eq., 89.2 mg, 0.484 mmol) and 4-(2—cyanoeth yny1)benzoic acid (1 eq., 82.9 mg, 0.484 mmol) in THF (4.84 mL) was cooled to 0°C and DCC (1 eq., 99.9 mg, 0.484 mmol) was added to the mixture. The ing solution was stirred at r.t. for 14h, then filtered and washed with EtzO. The filtrate was evaporated to give pentafluorophenyl 4—(2-cyanoethyny1)benzoate (120 mg, 0.358 mmol, 74% yield) as a white solid. 1H NMR (400MHz, 6) 5 = 8.29 (d, J = 8.3 Hz, 2H), 8.08 (d, J = 8.3 Hz, 2H).

Compound 17 can be used for a bio-conjugation method according to the invention.

Sodium 4-((4-(cyanoethynyl)benz0yl)0xy)-2,3,5,6-tetraflu0r0benzenesulfonate (18): 4” ¢ ¢ F NaO3S F 16 18 To the solution of 4-(2—cyanoethyn—1-yl)benzoic acid (1 eq., 54.2 mg, 0.317 mmol) and sodium 6-tetrafluorohydroxybenzenesulfonate (1 eq., 84.9 mg, 0.317 mmol) in dry DMF (0.792 mL) was added DCC (1 eq., 65.3 mg, 0.317 mmol) . The resulting mixture was stirred at r.t. for 36h, then cooled to 0°C, stirred for 1h, filtered and washed with 0.8 mL of dry DMF. The filtrate was diluted with 16 mL of EtzO, stirred for 15 min for complete crystallization and the precipitate was filtered to give sodium 4-((4-(cyanoethynyl)benzoyl)oxy)-2,3 ,5 ,6-tetrafluorobenzenesulfonate (72 .5 mg, 0.172 mmol, 54% yield) as a white solid. 1H NMR (400MHz, DMSO-ds) 8 = 8.31 (d, J = 6.3 Hz, 2H), 8.09 (d, J = 6.3 Hz, 2H).

Compound 18 can be used for a bio—conjugation method according to the invention.

WO 2015001117 41 N-((1-(4-(cyanoethynyl)phenyl)-1H-1,2,3-triaz0lyl)methyl) (dimethylamin0)naphthalenesulf0namide (20): N” o o f: N.]/\Hw o Og-NH 0 II —> + N \ o / || N // 19 N 20 5-(dimethylamino)-N-(propynyl)naphthalenesulfonamide (1 eq., 395 mg, 1.37 mmol) and 3—(4-azidophenyl)prop-2—ynenitrile (1 eq., 230 mg, 1.37 mmol) were solubilized in tBuOH (6.91 mL). To this mixture was added a solution of copper e pentahydrate (10 %, 34.2 mg, 0.137 mmol) in 0.5 mL of water followed by the solution of sodium ascorbate (0.5 eq., 135 mg, 0.685 mmol) in 0.5 mL of water. The resulting solution was stirred for 2h and then concentrated on rotary evaporator. The residue was extracted with DCM. The c layer was washed with saturated aqueous solution of NH4C1 and with water, dried over MgSO4 and evaporated to give 20 (544 mg, 1.19 mrnol, 87% yield) as a green solid. 1H NMR (400MHz, DMSO-ds) 5 = 8.59 (br. s., 1H), 8.34 (d, J = 7.3 Hz, 1H), 8.33 (s, 1H) 8.26 (d, J: 8.8 Hz, 1H), 8.13 (d, J= 7.3 Hz, 1H), 8.00 (d, J: 8.8 Hz, 2H), 7.83 (d, J: 8.8 Hz, 2H), 7.61 — 7.51 (m, 2H), 7.18 (d, J: 7.5 Hz, 1H), 4.21 (s, 2H), 2.71 (s, 6H). 13C NMR (101MHz, DMSO-ds) 8 = 151.2, 144.8, 138.4, 135.7, 135.6, 129.4, 128.9, 128.8, 128.6, 127.8, 123.4, 121.3, 119.9, 119.0, 116.0, 114.9, 105.3, 82.5, 63.1, 44.9, 37.6.

Compound 20 can be used for a ion method (with dyes, for instance) according to the invention. 3-(4-is0thiocyanat0phenyl)propiolonitrile (21): WO 20151001117 42 //N //N é i Cl C] é NaHCO3, 0 Silt H2” N 0°C, 10 min In a 50 mL RB flask, a solution of sodium hydrogen carbonate (886 mg, 10.55 mmol) in mL water was stirred for 10 min and to it dichloromethane (10 mL) was added followed by 3-(4-amin0phenyl)pr0pynenitrile (500 mg, 3.52 mmol). The reaction mixture was cooled to 0°C, thiophosgene (402 uL, 5.28 mmol) was introduced dropwise over a period of 30 min and continuously stirred at room temperature for 1 h.

The organic phase was separated and dried over ous MgSO4. Concentration of the solution afforded pure 21 (609 mg, 3.31 mmol, 94% yield) in form of yellow solid. 1H NMR (400MHz, ACETONITRILE-ds) 8 = 7.71 (d, J = 8.5 Hz, 2H), 7.37 (d, J = 8.5 Hz, 2H).

Compound 21 can be used for a bio-conjugation method according to the invention. utyl (1-((4-(cyan0ethynyl)phenyl)amin0)thi0x0-6,9,12-tri0xa azapentadecanyl)carbamate (22): S o & NJLNMO/Vowo/WNAOk // H H H 21 22 tert-Butyl (3-(2-(2-(3—amin0pr0p0xy)ethoxy)eth0xy)pr0pyl)carbamate (1 eq., 91.5 mg, 0.271 mmol) was dissolved in of DCM (2 mL) and cooled to 0°C. To this solution 3-(4- is0thiocyanatophenyl)pr0pynenitrile (1 eq., 50 mg, 0.271 mmol) in 1 mL of DCM was slowly added and the mixture was d for 30 min. The reaction mix was concentrated to 1 mL and the residue was purified by flash chromatography (DCM/MeOH gradient, 100/0 to 90/10) to give tert-butyl (1-((4- (cyanoethynyl)phenyl)amin0)—I -thi0x0-6, 9, 12—tri0xa—2-azapentadecan-I5-yl)carbamate (126 mg, 0.25 mmol, 92% yield) as a yellow oil.

WO 20151001117 43 1H NMR (400MHz, METHANOL-d4) 5 = 7.66 (s, 4H), 3.65 — 3.54 (m, 12H), 3.50 (t, J = 6.1 Hz, 2H), 3.12 (t, J = 6.8 Hz, 2H), 1.91 (quin, J = 6.1 Hz, 2H), 1.72 (quin, J = 6.4 Hz, 2H), 1.45 (s, 9H). 13c NMR (101MHz, METHANOL—d4) 5 = 182.0, 158.5, 144.6, 135.6, 106.4, 84.8, 80.0, 71.6, 71.5, 71.3, 71.3, 70.0, 68.2, 63.0, 38.8, 31.0, 29.8, 29.0 4-(cyan0ethynyl)benz0yl chloride (23): N\\ N\\ % % OH CI 16 23 4-(2-cyanoeth-I-yn-I—yl)benzoic acid (1 eq., 30 mg, 0.175 mmol) was ved in DCM (2 mL) and SOC12 (31.5 eq., 400 uL, 5.51 mmol) was added. The e was stirred at reflux until the solid tely dissolved and then evaporated to give pure 23 (29.6 mg, 0.156 mmol, 89% yield) as a white solid. 1H NMR (400MHz, CHLOROFORM-d) 8 = 8.08 (d, J = 8.3 Hz, 2H), 7.67 (d, J: 8.3 Hz, 2H).

Compound 23 can be used for a bio-conjugation method according to the invention. tert-butyl (1-(4-(cyanoethynyl)phenyl)0x0-6,9,12-tri0xaazapentadecan yl)carbamate (24): N \ \ \ Q —> N\/\/ \/\O/\/ \/\/O O H 0 CI \n/ \'< O O 23 24 tert-Bulyl (3 —(2-(2-(3-amin0pr0p0xy)ethoxy)ethoxy)propyl)carbamate (1 eq., 50 mg, 0.156 mmol) and NEt3 (5 eq., 78.9 mg, 0.108 mL, 0.78 mmol) were dissolved in 1 mL of DCM and cooled to -78°C. To this solution was slowly added 23 (1 eq., 29.6 mg, 0.156 mmol) in 1 mL of DCM. The mixture was gradualy warmed to r.t. and stirred for WO 20151001117 44 2h. The reaction mix was then injected into flash chromatography column and eluted with DCM/MeOH (gradient 100/0 to 90/10) to give pure 24 (40.6 mg, 0.086 mmol, 55 %) as a yellow oil. 1H NMR (400MHz, METHANOL-d4) 8 = 7.92 (d, J = 8.3 Hz, 2H), 7.82 (d, J = 8.3 Hz, 2H), 3.72 - 3.45 (m, 14H), 3.12 (t, J = 6.8 Hz, 2H), 1.90 (quin, J = 6.3 Hz, 2H), 1.72 (quin, J = 6.4 Hz, 2H), 1.44 (s, 9H). 4-(cyan0ethynyl)-N-(15-0x0-4, 7,10-tri0xaazan0natriaconta-24,26-diyn yl)benzamide (25): 16 ~\\\ 0 ‘\—0 NH 4-(2-cyanoethynyl)benzoic acid (1 eq., 29.7 mg, 0.173 mmol) was suspended in DCM and SOClz (39.8 eq., 820 mg, 0.5 mL, 6.89 mmol) was added. The mixture was stirred at reflux for 1.5h, evaporated, dissolved in DCM, and added to the solution of N- (3 - {2-[2-(3 -aminopropoxy)ethoxy]ethoxy}propyl)pentacosa-10, 12-diynamide (1 eq. , 100 mg, 0.173 mmol) and TEA (4 eq., 70.2 mg, 0.0964 mL, 0.693 mmol) in DCM at -78°C. The ing e was stirred at r.t. for 1h and evaporated. The residue was purified by flash chromatography eOH : 10/0 to 9/ 1) to give the desired product (35.4 mg, 0.0485 mmol, 28% yield) as a yellow 011. 1H NMR z, CHLOROFORM—d) 8 = 7.90 (d, J = 8.3 Hz, 2H), 7.67 (d, J: 8.3 Hz, 2H), 7.48 (br. s, 1H), 6.18 (br. s, 1H), 3.71 - 3.45 (m, 14H), 3.32 (t, J: 6.0 Hz, 2H), 2.23 (t, J: 6.8 Hz, 4H), 2.15 (t, J = 7.5 Hz, 2H), 1.90 (td, J: 6.0, 11.7 Hz, 2H), 1.73 (quin, J: 6.1 Hz, 2H), 1.65 - 1.42 (m, 6H), 1.41 - 1.32 (m, 4H), 1.32 - 1.19 (m, 22H), 0.88 (t, J= 6.8 Hz, 3H).

Compound 25 can be used for the labeling (such as photolabeling) method according to the invention or for binding and/or immobilizing compounds.

WO 20151001117 45 Ethyl (4-(cyan0ethynyl)phenyl)carbamate (26): 16 26 To a solution of triphosgene (1 eq., 49.5 mg, 27.8 uL, 0.167 mmol) in DCM (4 mL) was added a solution of 3-(4-aminophenyl)propynenitrile (3 eq., 71.1 mg, 0.5 mmol) in DCM (1 mL). Then triethylamine (6 eq., 101 mg, 138 uL, 1 mmol) in 1 mL of DCM was added dropwise. The mixture was stirred for 15 min allowing the formation of isocyanate intermediate and then ethanol (0.1 mL) was added dropwise. The reaction mixture was d for 1h then washed with 2x5mL of water and evaporated. The residue was d by flash chromatography to give ethyl (4- (cyanoethynyl)phenyl)carbamate (102 mg, 0.48 mmol, 96% yield) as a white solid. 1H NMR (400MHz, CHLOROFORM-d) 8 = 7.56 (d, J = 8.5 Hz, 2H), 7.46 (d, J = 8.5 Hz, 2H), 6.79 (br. s., 1H), 4.26 (q, J= 7.0 Hz, 2H), 1.33 (t, J= 7.0 Hz, 3H). cyanoethynyl)phenyl)(propynyl)urea (27): N //N // //N é é é —’ —’ o\ i \ N N H2N C“N /H H 7 27 To a solution of triphosgene (1 eq., 49.5 mg, 27.8 uL, 0.167 mmol) in DCM (2 mL) was added a solution of 3—(4-aminophenyl)propynenitrile (3 eq., 71.1 mg, 0.5 mmol) in DCM (3 mL). Then triethylamine (6 eq., 101 mg, 138 uL, 1 mmol) was added, the mixture was stirred for 5 min and then were added propargylamine (4.69 eq., 43 mg, 50.1 uL, 0.782 mmol) and triethylamine (2 eq., 33.7 mg, 46.3 uL, 0.333 mmol) in 1 mL of DCM. The reaction mixture was d for 1h then washed with 5mL of water, dried over MgSO4 and concentrated. The residue was purified by flash chromatography (DCM/MeOH gradient) to give l-(4-(cyanoethynyl)phenyl)-3—(prop—2-yn-l—yl)urea (94.9 mg, 0.425 mmol, 85% yield) as a white solid.

WO 20151001117 46 1H NMR (400MHz, METHANOL-d4) 5 = 7.60 (d, J = 8.8 Hz, 2H), 7.52 (d, J = 8.8 Hz, 2H), 4.00 (d, J = 2.4 Hz, 2H), 2.61 (t, J = 2.4 Hz, 1H).

Compound 27 can be used for click chemistry according to the invention. prop-Z-yn-I-yl (4-(cyan0ethynyl)phenyl)carbamate (28): To a solution of triphosgene (1 eq., 49.5 mg, 27.8 uL, 0.167 mmol) in DCM (2 mL) was added a on of 3-(4-aminophenyl)prop—2-ynenitrile (3 eq., 71.1 mg, 0.5 mmol) in DCM (3 mL). Then triethylamine (6 eq., 101 mg, 138 uL, 1 mmol) was added. The mixture was stirred for 5 min and then were added 2-propynol (6 eq., 56.1 mg, 59.1 11L, 1 mmol) and triethylamine (2 eq., 33.7 mg, 46.3 uL, 0.333 mmol) in 1 mL ofDCM.

The reaction mixture was d for 1h then washed with 5mL of water, dried over MgSO4 and concentrated. The e was purified by flash chromatography (Cyclohexane/EtOAc nt) to give prop—2-yn-I —yl (4- (cyanoethynyl)phenyl)carbamate (104 mg, 0.465 mmol, 93% yield) as a white solid. 1H NMR (400MHz, CHLOROFORM—d) 8 = 7.57 (d, J = 8.6 Hz, 2H), 7.48 (d, J: 8.6 Hz, 2H), 4.80 (d, J: 2.3 Hz, 2H), 2.54 (t, J: 2.3 Hz, 1H).

Compound 28 can be used for click chemistry according to the invention. bicycl0[6.1. 0]n0nynylmethyl (4-(cyan0ethynyl)phenyl)carbamate (29): _, OJL” 7 29 To a solution of triphosgene (1 eq., 34.8 mg, 19.5 uL, 0.117 mmol) in DCM (4 mL) was added a solution of 3-(4-aminophenyl)propynenitrile (3 eq., 50 mg, 0.352 mmol) in DCM (1 mL). Then triethylamine (6 eq., 71.2 mg, 97.8 uL, 0.703 mmol) was added W0 20151001117 47 dropwise. The mixture was d for 5 min at r.t. and then bicyclo[6.l.0]nonyn ylmethanol (3 eq., 52.8 mg, 0.352 mmol) and triethylamine (2 eq., 23.7 mg, 32.6 uL, 0.234 mmol) were added in 1 mL of DCM. The reaction e was stirred at r.t. for 2 hours. After full conversion was confirmed by HPLC the mixture was trated to 1 mL volume and purified by flash chromatography (cyclohexane/EtOAc gradient) to give bicyclo[6.l.0]nonyn—9-ylmethyl (4-(cyanoethynyl)phenyl)carbamate (68.3 mg, 0.215 mmol, 183 %) as a white solid. 1H NMR (400MHz, CHLOROFORM-d) 8 = 7.55 (d, J = 8.8 Hz, 2H), 7.47 (d, J: 8.8 Hz, 2H), 7.09 (br. s, 1H), 2.38 - 2.14 (m, 6H), 1.67 - 1.51 (m, 2H), 1.42 (quin, J: 8.7 Hz, 1H), 1.04 - 0.91 (m, 2H) Compound 29 can be used for click chemistry (such as strain-promoted click) according to the invention. 3-(4-((trimethylsilyl)ethynyl)phenyl)pr0pyn0l (30a): /©/| / >Si \ /<j/\QHé I /S||_ 303 Product was synthesized according to general procedure B for coupling. Yield : 99%. 1H NMR (400MHz, CHLOROFORM-d) 8 = 7.41 (d, J = 8.4 Hz, 2H), 7.36 (d, J = 8.4 Hz, 2H), 4.50 (d, J= 5.5 Hz, 2H), 1.89 (t, J= 5.5 Hz, 1H), 0.25 (s, 9H). 3-(4-(trimethylszlyl)ethynyl)phenyl)pr0p10l0nltrlle (30): 30a 30 t was synthesized according to general procedure of MnOz-oxidation. Reaction time: 3 hours; yield: 29%. 1H NMR (400MHz, CHLOROFORM-d) 8 = 7.55 (d, J = 8.4 Hz, 2H), 7.48 (d, J = 8.4 Hz, 2H), 0.27 (s, 9H).

WO 2015001117 48 13C NMR (101MHz, CHLOROFORM-d) 8 = 133.2, 132.2, 126.9, 117.1, 105.3, 103.4, 99.4, 82.3, 64.5, -0.3. 3,3 '-(5-amin0-I,3-phenylene)dipr0piolonitrile (31): Product was synthesized ing to general procedure of MnOz-oxidation. Reaction time: 3 hours; yield: 11%. 1H NMR (400MHz, CHLOROFORM-d) 5 = 7.20 (t, J = 1.3 Hz, 1H), 6.98 (d, J = 1.3 Hz, 2H), 4.02 (br. s., 2H). 13C NMR (101MHz, CHLOROFORM-d) 8 = 147.1, 127.5, 121.6, 119.5, 105.0, 81.0, 63.6.

Compound 31 can be used for rebridging (diAPN) according to the invention. 3-(4-(4, 4,5,5-tetramethyl-1,3,2-di0xab0rolanyl)phenyl)propiolonitrile (32): D// OH O\ —> '13 /[:/ O 0‘s Product was sized according to general procedure of xidation. Reaction time: 4 hours; yield: 63%. 1H NMR (400MHz, CHLOROFORM-d) 8 = 7.84 (d, J = 8.2 Hz, 2H), 7.60 (d, J: 8.2 Hz, 2H), 1.36 (s, 12H). 3,3'-(1,2-Phenylene)dipropiolonitrile (33): propargylic / I / alcoho|,Cu|, // PdCI2(PPh3)2I OH Mn02, NHs I —> — —> DIPEA, DMF M9804, IPA, THF \ 33a 33 333: 3,3'-(1,2-Phenylene)bis(propyn-l-ol). wo 20157001117 49 To the degased solution of iodobenzene (1 eq., 661 mg, 0.262 mL, 2 mmol) and propargylic alcohol (2.3 eq., 272 uL, 4.61 mmol) in butyl amine (15.8 mL), Pd(PPh3)4 (4%, 92.6 mg, 0.0801 mmol) was added and the obtained reaction mass was refluxed overnight. Solvents were ated and the obtained crude product was purified by flash tography (20 minutes gradient EtOAc/Cyclohexane) to yield 333 (150 mg, 0.8 mmol, 40 %) as a brownish solid. 1H NMR (400 MHz, METHANOL-d4) 8 7.38 - 7.53 (m, 2H), 7.25 — 7.38 (m, 2H), 4.48 (s, 4H); 13C NMR (101 MHz, METHANOL-d4) d 135.6, 131.9, 129.2, 95.6, 86.6, 53.9; ESI-MS: C12H1102+ [M+H]+, 187.1; found 187.1. 33: 3,3'-(1,2-Phenylene)dipropiolonitrile.

The compound was obtained as the only product of the standard Mn02 oxidation protocol. Reaction time: 75 minutes. Brown solid, yield: 42%. 1H NMR (400 MHz, METHANOL-d4) 8 7.89 (dd, J: 3.30, 5.80 Hz, 2H), 7.73 (dd, 12 3.30, 5.80 Hz, 2H); 13C NMR (101 MHz, METHANOL—d4) 8 136.0, 133.5, 126.5, 105.5, 80.2, 67.2; GC-ESI-MS: C12H5N2+ [M+H]+, 177.0; found 177.0. 3,3'-(1,3-Phenylene)dipropiolonitrile (34): propargylic l Cul PcICI2P(Ph) MnOz NHa DIPEA DMF MgSO4 IPA THF 34a: 1,3-Phenylene)bis(propyn-l-ol).

Same procedure as for the synthesis of 33a. Brownish solid, yield: 55%. 1H NMR (400 MHz, METHANOL—d4) 8 7.47 (s, 1H), 7.36 - 7.43 (m, 2H), 7.29 - 7.36 (m, 1H), 4.41 (s, 4H); 13C NMR (101 MHz, METHANOL—d4) 8 135.3, 132.5, 129.8, 124.8, 89.7, 84.5, 51.2; ESI-MS: C12H1102+ [M+H]+, 187.1; found 187.0. 34: 3,3'-(1,3-Phenylene)dipropiolonitrile.

The compound was obtained as the only product of the rd MnOz oxidation protocol. Reaction time: 2 hours. Brown solid, yield: 35%.

W0 20151001117 50 1H NMR (400 MHz, METHANOL-d4) 5 8.10 (d, J = 1.50 Hz, 1H), 7.93 (dd, J = 1.50, 8.00 Hz, 1H), 7.63 (t, J: 8.00 Hz, 2H); 13C NMR (101 MHz, METHANOL-d4) 5 139.3, 137.8, 131.2, 120.0, 105.7, 81.7, 64.2; GC-ESI-MS: ClesNz+ [M+H]+, 1770, found 177.1. 3,3'-(1,4-Phenylene)dipropiolonitrile (35): Br propargylic alcohol Cul PdCI2(PPh3)2 MnOZ NH3 DIPEA, DMF MgSO4 IPA, THF 353: 3,3'-(1,4-Phenylene)bis(prop-2—ynol).

Sarne procedure as for the synthesis of 333, but refluxed for 72 hours. Brownish solid, yield: 35%. 1H NMR (400 MHz, METHANOL-d4) 8 7.39 (s, 4H), 4.41 (s, 4H); 13C NMR (101 MHz, METHANOL-d4) 5 132.6, 124.3, 101.4, 90.8, 84.9, 51.2; : C12H1102+ , 187.1; found 187.1. : 1,4-Phenylene)dipropiolonitrile.

The nd was obtained as the only product of the standard MnOz oxidation protocol. Reaction time: 2 hours. Brown solid, yield: 19%. 1H NMR (400 MHz, METHANOL-d4) 6 7.94 (s, 4H); 13C NMR (101 MHz, METHANOL—d4) 8 135.0, 121.6, 105.5, 82.0, 65.9; GC-ESI-MS: C12H5N2+ [M+H]+, 177.0; found 177.0.

Cornpounds 33-35 can be used for rebridging (diAPN) according to the invention. tert-butyl (S)((tert-butoxycarbonyl)amino)(4- (((triflu0r0methyl)sulfonyl)0xy)phenyl)pr0panoate (36b): WO 20151001117 51 OH O\S//O F d’XF >L O F CAN >L JOL 07< o H H Oj< o 0 To a cooled to 0 °C solution of tert-butyl 2-{[(tert-butoxy)carbony1]amino}(4- hydroxypheny1)propanoate (1 eq., 518 mg, 1.54 mmol) in pyridine (2.5 mL), triflic ide (1.1 eq., 476 mg, 0.28 mL, 1.69 mmol) was added dropwise over 20 minutes (using e presser). The resulting dark solution was let to warm up to room temperature, poured into water (10 mL), and extracted with ethyl ester (15 mL). The ether extract was washed sequentially with water (5 mL), 1N HCl (2x5 mL), water (5 mL), brine (5 mL), dried over MgSO4, and evaporated to give the targeted product (614 mg, 1.31 mmol, 85 %) as a dark-red oil. The product was used in the next step without fiarther purification. 1H NMR (400 MHZ, CHLOROFORM-d) 8 7.03 - 7.18 (m, 3H), 6.82 - 7.03 (m, 2H), 4.87 (d, J = 7.28 Hz, 1H), 4.24 (d, J: 7.03 Hz, 1H), 2.65 - 2.95 (m, 2H), 1.17 (s, 9H), 1.21 (s, 9H). 13C NMR (101 MHz, CHLOROFORM-d) 8 170.5, 148.5, 137.3, 131.3, 121.1, 120.3, 117.1, 82.5, 80.0, 54.7, 38.1, 28.3, 27.9. tert-butyl (S)((tert-but0xycarb0nyl)amin0)(4-(3-hydr0xypr0pyn yl)phenyl)pr0pan0ate (36a): O\S/§D F o" f.

XOAHO —. #0 O)L OW< H OK O 0 36b 36a To a solution of phenoltryphlate (1 eq., 136 mg, 0.291 mmol) in morpholine (1 mL) were uently added PdC12(PPh3)2 (5 %, 10.2 mg, 0.0145 mmol), CuI (10 %, .53 mg, 0.0291 mmol), and propargylic alcohol (2 eq., 32.6 mg, 0.0343 mL, 0.581 W0 20151001117 52 mmol). The obtained reaction mixture was degassed and heated at 60 0C for 24 hours.

The resulting black solution was poured into water (10 mL), extracted with EtOAc (3X10 mL). The united organic layers were washed with 1N HCl (2X10 mL), water (1X10 mL), dried over MgSO4 and evaporated to give crude product, which after purification by flash chromatography gave the targeted product (8.73 mg, 0.0232 mmol, 8 %) as a ish solid. 1H NMR (400 MHz, METHANOL-d4) 5 7.30 = 7.78 Hz, 2H), 7.14 - 7.45 (m, J - 7.30 (m, J = 8.03 Hz, 2H), 4.40 (s, 2H), 4.18 = 6.27, 13.80 Hz, - 4.32 (m, 1H), 3.06 (dd, J 1H), 2.91 (dd, J: 8.66, 13.68 Hz, 1H), 1.45 - 1.53 (m, 1H), 1.42 (d, J: 3.26 Hz, 19H). tert-Butyl 2-((tert-butoxycarbonyl)amin0)(4-(cyanoethynyl)phenyl)pr0pan0ate (36): O 0 OX OX HN o —’ “N 0 HO é Y 7 Y 0% N’ 0% 36a 36 Product was synthesized according to general ure of MnOz-oxidation. Reaction time: 2 hours; yield: 56%. 1H NMR (400MHz, FORM-d) 8 = 7.54 (d, J = 8.2 Hz, 2H), 7.24 (d, J: 8.2 Hz, 2H), 5.05 (d, J: 7.3 Hz, 1H), 4.46 (td, J: 6.1, 7.3 Hz, 1H), 3.14 (dd, J: 6.1, 13.7 Hz, 1H), 3.05 (dd, J: 6.1, 13.7 Hz, 1H), 1.42 (s, 9H), 1.41 (s, 9H). 13C NMR (101MHz, CHLOROFORM-d) 8 = 170.3, 154.9, 141.4, 133.4, 130.1, 115.9, 105.5, 82.9, 82.5, 79.9, 63.2, 54.5, 38.8, 28.3, 27.9.

Compound 36 can be used for purification and/or immobilization according to the invention. 4-(cyan0ethynyl)-N-(2-(2-(2-(5-((3aS,4S,6aR)0x0hexahydr0-1H-thien0[3,4- d]imidaz0lyl)pentanamido)ethoxy)ethoxy)ethyl)benzamide (3 7) WO 20151001117 53 HTNH H 0 “\\/\)J\N/\/O\/\O/\/H H8 0 To the solution of N—(2-(2-(2-aminoethoxy)eth0xy)ethyl)((3aS,4S,6aR) 0x0hexahydr0—1H-thien0[3,4—d]imidazolyl)pentanamide (1 eq., 222 mg, 0.593 mmol) in dry DMF (1 mL) was added sodium 4-((4-(cyanoethynyl)benz0yl)0xy)-2,3,5,6- tetrafluorobenzenesubconate (1.2 eq., 300 mg, 0.712 mmol) and DIEA (5.] eq., 39] mg, 0.5 mL, 3.03 mmol). The mixture was d at r.t. for 3 hours and then purified by semi-preparative HPLC to give the desired product (68.8 mg, 0.13 mmol, 22% yield) as a yellow oil. 1H NMR (400MHz ,METHANOL-d4) 5 = 7.92 (d, J = 8.5 Hz, 2 H), 7.81 (d, J: 8.5 Hz, 2 H), 4.49 (dd, J = 4.8, 7.8 Hz, 1 H), 4.30 (dd, J: 4.5, 7.8 Hz, 1 H), 3.71 — 3.56 (m, 8 H), 3.54 (t, J: 5.5 Hz, 2 H), 3.34 (t, J: 5.5 Hz, 2 H), 3.24 - 3.14 (m, 1 H), 2.92 (dd, J: 4.8, 12.8 Hz, 1 H), 2.70 (d, J: 12.8 Hz, 1 H), 2.19 (t, J: 7.4 Hz, 2 H), 1.78 — 1.50 (m, 4 H), 1.48 - 1.35 (m, 2 H). 13C NMR (101MHz ,METHANOL-d4) 5 = 176.3, 168.8, 166.2, 138.9, 135.0, 129.1, 121.5, 105.9, 83.1, 71.5, 71.4, 70.7, 70.6, 64.6, 63.5, 61.8, 57.1, 41.2, 40.4, 36.9, 29.9, 29.6, 27.0.

W0 01117 54 2-((4-((4-(Cyanoethynyl)phenyl)amino)oxobutyl)-amino) oxoethyl)tris(2,4,6-trimethoxyphenyl)phosphonium roacetate (38): NH2 0 propargylic alcohol. OWNHBOC Boo GABA- WNHBOCPd(PPh3)2C|2 —,HN _, EDC, TEA, DMAP DIPEA DCM, 0°C THF, 25°C /0 J, O MnOZV 3‘ NH3(|PA)V 3“ 0‘ M91304, P 0’ THF O O BocHN _ \ TMPP-Ac—OSu O NH 38 38a 38b 38d: utyl (4-((4-iodophenyl)amino)-4—oxobutyl)carba-mate.

To the cooled to 0°C solution of Boc-GABA (1 eq., 0.928 g, 4.57 mmol), TEA (3 eq., 1.39 g, 1.9 mL, 13.7 mmol) and DMAP (0.05 eq., 0.0279 g, 0.228 mmol) in DCM (11.7 mL), EDC (1 eq., 0.875 g, 4.57 mmol) was added. The obtained reaction mass was stirred for another 10 minutes at 0°C, an ice bath was removed, and p-iodoaniline (1 eq., 1 g, 4.57 mmol) was added and the reaction was left overnight at 25°C. The obtained reaction mass was washed with 1M HCl (2x20 rnL), water (1X20 mL), and dried over Na2S04 to give 38d (1125 mg, 2.79 mmol, 61 %), which was used without fiarther purification. 1H NMR (400 MHz, CHLOROFORM-d) 8 9.04 (br. s., 1H), 7.58 = 8.50 — 7.72 (m, J Hz, 2H), 7.37 = 8.50 Hz, 2H), 4.81 - 7.51 (m, J (br. s., 1H), 3.27 (rn, 2H), 2.30 - 2.50 (m, 2H), 1.88 (m, 2H), 1.49 (s, 9H); 13C NMR (101 MHz, CHLOROFORM—d) 8 174.2, 157.4, 137.8, 120.9, 120.0, 87.3, 77.0, 33.1, 32.8, 28.4, 26.0; ESI-MS: C15H22N203+ [M+H]+, 405.0; found 405.1.

WO 2015001117 55 38c: tert-Butyl -(3-hydroxypropynyl)phenyl)-amino) oxobutyl)carbamate. sised following the protocol B for Sonogashira ng. Yellowish solid, yield: 79%. 1H NMR (400 MHz, METHANOL-d4) 5 7.54 = 8.50 Hz, 2H), 7.34 - 7.58 (m, J - 7.38 (m, J = 8.50 Hz, 2H), 4.40 (s, 2H), 3.13 (t, J: 6.90 Hz, 2H), 2.41 (t, J: 740 Hz, 2H), 1.81-1.89 (m, 2H), 1.44 (s, 9H); 13C NMR (101 MHz, OL—d4) 8 174.0, 158.6, 140.1, 133.2, 120.8, 119.5, 88.3, 85.3, 80.1, 51.3, 40.9, 35.3, 28.8, 27.1; ESI-MS: C18H25N204+ [M+H]+, 332.1; found 332.0. 38b: tert-Butyl (4-((4-(cyanoethynyl)phenyl)amino)0X0butyl)carbamate.

Synthesised using rd protocol of Mn02 oxidation. Reaction time: 1 hour. White solid, yield: 85%. 1H NMR (400 MHz, METHANOL—d4) 5 7.61 = 8.80 Hz, 2H), 7.54 - 7.65 (m, J - 7.59 (m, J: 8.50 Hz, 2H), 3.04 (t, J: 6.85 Hz, 2H), 2.34 (t, J: 7.40 Hz, 2H), 1.74-1.81 (m, 2H), 1.34 (s, 9H); 13C NMR (101 MHz, METHANOL-d4) 8 174.3, 159.1, 143.8, 135.7, 120.8, 112.8, 106.3, 84.6, 62.7, 40.8, 35.3, 34.8, 28.8, 26.9; ESI—MS: C18H22N303+ [M+H]+, 328.1; found 328.1. 383: 4-((4-(Cyanoethynyl)phenyl)amino)oxobutanaminium trifluoroacetate.

To a suspension of 38b (1 eq., 62.8 mg, 0.192 mmol) in DCM (1 mL), TFA (20 eq., 285 uL, 3.83 mmol) was added and the obtained solution was stirred at 25°C for 30 minutes.

The target product 383 (TFA salt, 65.0 mg, 0.19 mmol, 99 %) was obtained after the evaporation of the on mass and was used without further purification in the next step. 1H NMR (400 MHz, METHANOL-d4) 5 7.71 = 9.15 Hz, 2H), 7.63 - 7.79 (m, J - 7.70 (m, J = 9.15 Hz, 2H), 3.04 (t, J= 6.80 Hz, 2H), 2.6 (t, J= 7.05 Hz, 2H), 1.98-2.08 (m, 2H); 13C NMR (101 MHz, METHANOL-d4) 8 173.1, 143.6, 135.7, 120.7, 112.9, 106.2, 84.5, 62.7, 40.4, 34.5, 24.0; ESI-MS: C13H14N30+ [M+H]+, 228.1; found 228.1. 38: (2-((4-((4-(Cyanoethynyl)phenyl)amino)0X0butyl)amino) oxoethyl)tris(2,4,6-trimethoxyphenyl)phosphonium trifluoroacetate.

To the solution of 383 (1 eq., 10.1 mg, 0.0296 mmol) in DMF (250 uL), TEA (1 eq., 4 uL, 0.0296 mmol) was added. TMPP-Ac-OSu (1 eq., 22.7 mg, 0.0296 mmol) was added to the obtained solution and the reaction mass was for 15 minutes at room temperature.

W0 20151001117 56 The crude product was purified by HPLC to isolate 38 (9.9 mg, 0.0126 mmol, 42 %) as a main product. 1H NMR (400 MHz, METHANOL-d4) 5 7.44 - 7.59 (m, 4H), 6.13 (d, J: 4.52 Hz, 6H), 3.75 (s, 9H), 3.50 (s, 18H), 3.00 (td, J= 7.91, 15.31 Hz, 2H), 2.26 (t, J: 6.90 Hz, 2H), 1.64-1.75 (m, 2H), 1.25-1.43 (m, 2H); 13C NMR (101 MHz, METHANOL—d4) , 167.4, 167.4, 165.3, 143.6, 135.8, 120.6, 112.8, 106.3, 92.2 (d, J: 8 Hz), 84.5, 62.7, 56.5, 56.2, 37.5, 29.4 (d, J: 64 Hz), 27.9, 27.7, 24.9; ESI-HRMS: C42H47N3011P+ [M]+, 800.29427; found 800.29401. (5-((4-(Cyanoethynyl)phenyl)amino)oxopentyl)tris(2,4,6- trimethoxyphenyl)phosphonium bromide (39): 0 Br lowBr propargylic YWalcohol, HN Pd(PPh3)2C|2 —’ MOI —’ DIPEA DIPEA \ DCM THF \ 905$ MnOz‘ NH3 (IPA), M9304, YN OWE I N\©\ .flToluene, 60°C\\N 39 HN\<j:a\\\N 39d: 5-Bromopentanoyl chloride.

Degassed solution of 5-brornopentanoic acid (1 eq., 2.85 g, 15.7 mmol) and SOC12 (1 eq., 1.87 g, 1.14 mL, 15.7 mmol) in DCM (50 mL) was refluxed for 3 hours. The obtained reaction mass was evaporated under reduced pressure to give 39d (3.11 g, 100%) as a yellowish oil. The crude product was used in the next step without purification. 39c: S-Bromo-N-(4-iodophenyl)pentanamide.

Solution of 39d (1 eq., 3.11 g, 15.7 mmol) in DCM (50 mL) was poured into a cooled to -78°C on of 4-iodoaniline (1 eq., 3.45 g, 15.7 nlrnol) and DIPEA (1 eq., 2.03 g, 2.6 WO 2015001117 57 mL, 15.7 mmol) in DCM (50 mL). Obtained reaction mass was allowed to warm to room temperature, stirred for another 30 min, washed with 1N HCl (2X25 mL), water (1x25 mL), dried over Na2S04 and evaporated to give 39c (5.60 g, 14.66 mmol, 93%) as brown solid. 1H NMR (400 MHz, METHANOL-d4) 5 7.62 - 7.66 (m, 2H), 7.38 — 7.43 (m, 2H), 3.50 (t, J= 6.53 Hz, 2H), 2.42 (t, J: 7.28 Hz, 2H), 1.81 - 1.98 (m, 4H), 1.37 - 1.42 (m, 1H); 13C NMR (101 MHz, METHANOL—d4) 5 174.0, 140.5, 138.9, 123.1, 87.6, 36.9, 33.8, 33.4, 25.3; ESI-MS: C11H14BrINO+ [M+H]+, 381.9; found 381.8. 39b: S-Bromo-N-(4-(3-hydroxyprop-l-ynyl)phenyl)pentanamide: sised following the protocol A for Sonogashira coupling. Brown solid, yield: 92%. 1H NMR (400 MHz, METHANOL-d4) 57.49 = 8.53 Hz, 2H), 7.32 - 7.63 (m, J - 7.43 (m, J = 8.53 Hz, 2H), 4.40 (s, 2H), 4.26 (s, 1H), 3.50 (t, J = 6.53 Hz, 2H), 2.43 (t, J = 7.15 Hz, 2H), 1.90 - 2.04 (m, 2H), 1.74 - 1.90 (m, 2H), 1.32 (s, 1H); 13C NMR (101 MHz, METHANOL-d4) 5173.9, 140.0, 133.1, 120.7, 119.6, 88.2, 85.2, 51.2, 36.8, 33.7, 33.3, 25.3; ESI—MS: C14H17BrNO+ , 3100; found 310.0. 393: 5-Brom0-N-(4-(cyanoethynyl)phenyl)pentanamide. 2M solution of NH3 (4 eq., 94.8 mg, 5.56 mmol) in IPA and anhydrous MgSO4 (15 eq., 2511 mg, 20.9 mmol) were added to a stirred solution of 39b (1 eq., 431 mg, 1.39 mmol) in THF (3.42 mL). Activated MnOz (15 eq., 1814 mg, 20.9 mmol) was added to the solution and the resulting mixture was stirred at room temperature for 4 hours (controlled by TLC, no more starting alcohol; NB: too long reaction time gives ysis product), diluted with DCM (13 mL). The mixture was filtered, washed thoroughly with DCM and the ed es were concentrated under reduced pressure. The solid residue was purified by flash chromatography (EtOAc-cyclohexane, min gradient from 0 to 100% of EtOAc) to give 39 as a white solid (288 mg, 0.946 mmol, 68 %). 1H NMR (400 MHz, METHANOL-d4) 57.69 = 8.78 Hz, 2H), 7.59 - 7.79 (m, J - 7.69 (m, J = 8.78 Hz, 2H), 3.50 (t, J = 6.53 Hz, 2H), 1.79 - 1.99 (m, 4H), 1.26 (t, J = 7.15 Hz, 2H); 13C NMR (101 MHz, METHANOL-d4) , 143.8, 135.7, 120.7, 112.8, 106.2, 101.4, 84.6, 37.0, 33.7, 33.4, 25.2. ESI-MS: C14H14BrN20+ [M+H]+, 304.0; found 304.0.

W0 20151001117 5 8 39: (5-((4-(Cyanoethynyl)phenyl)amino)0X0pentyl)tris(2,4,6-trimethoxy— phenyl)phosphonium bromide. 39a (1 eq., 20 mg, 0.0655 mmol) and tris(2,4,6-trimethoxy—phenyl)phosphane (TMPP, 1.2 eq., 41.9 mg, 0.0786 mmol) were ved in dry toluene (1 mL) and stirred overnight at room temperature. 39 (TFA salt, 22 mg, 39%) was obtained after reversephase HPLC as a white solid. 1H NMR (400 MHz, METHANOL-d4) 8 7.51—7.55 (m, 4H), 6.13 (d, J = 4.77 Hz, 6H), 3.75 (s, 9H), 3.50 (s, 18H), 3.00 (td, J= 6.90, 15.31 Hz, 2H), 2.26 (t, J: 6.90 Hz, 2H), 1.73 (m, 2H), 1.22 - 1.45 (m, 2H); 13C NMR (101 MHz, METHANOL-d4) 8 174.2, 167.4, 165.3, 143.6, 135.8, 120.6, 112.8, 106.2, 93.6, 92.3, 92.2, 84.5, 62.7, 56.3, 37.5, 29.7, 27.7, 24.9; ESI-HRMS: C41H46N2010P+ [M]+, 757.28846; found 757.29552. (4-(4-(Cyanoethynyl)benzamido)butyl)tris(2,4,6-trimethoxyphenyl)phosphonium trifluoroacetate (40): 1. SOCI2 ,A . HN/\/\Br 2. propargyllc HN/V\Br alcohol, HO NH2 Br 3)2C|2 O | —> —> DIPEA DIPEA o \ DCM, 0°C THF, 25°C \ 406 401) CH MnOZY NH3 (IPA), 0 g M9504, I Z:TF THF flP\—\O_;O HNMBr TMPP o Toluene 60°C \\\\ \\ 40c: N-(4-Bromobutyl)iodobenzamide. 4-iodobenzoic acid (1 eq., 1.45 g, 5.85 mmol) was heated at 110 °C in SOClz (9 eq., 3.8 mL, 52.6 mmol) until complete dissolving (around 15 min). Excess of SOClz was d in vacuo and obtained solid was poured into DCM (15 mL), cooled to -78 °C and DIPEA (3.1 eq., 3 mL, 18.2 mmol) was added under vigorous stirring. 3- Bromopropylamine romide (1.5 eq., 1.90 g, 8.77 mmol) was added to the obtained reaction mass was left stirring for 5 minutes still at -78 °C, let to warm up to room temperature, while stirring for another 20 minutes. Ethyl acetate (100 mL) was W0 01117 59 added with 1M HCl (5 mL), obtained solid was filtered (product), washed with water and dried to yield 40c (2.09 g, 5.67 mmol, 97 %) as a white solid. 1H NMR (400 MHz, METHANOL-d4) 5 7.85 (m, J = 8.40 Hz, 2H), 7.58 (m, J = 8.40 Hz, 2H), 3.48-3.56 (m, 4H), 2.12-2.23 (m, 2H); 13C NMR (101 MHz, METHANOL-d4) 8 160.1, 139.2, 136.0, 132.8, 102.4, 50.1, 43.2, 23.0; ESI-MS: C10H12BrINO+[M+H]+, 367.9; found 368.0. 40b: N-(4-Bromobutyl)(3-hydroxypropynyl)benzamide.

Synthesised following the protocol B for Sonogashira coupling. Brown solid, yield: 81%. 1H NMR (400 MHz, METHANOL-d4) 5 7.73 (m, J = 8.40 Hz, 2H), 7.38 (m, J = 8.40 Hz, 2H), 4.37 (t, J = 5.30 Hz, 2H), 4.34 (s, 2H), 3.51 (t, J= 5.80 Hz, 2H), 1.92-1.98 (m, 2H); 13C NMR (101 MHz, METHANOL-d4) 8 159.2, 134.2, 132.4, 128.2, 127.1, 91.2, 84.8, 67.2, 51.2, 43.3, 22.5; : C13H15BTNOZ+[M+H]+, 295.0; found 295.0. 403: N-(3-Bromopropyl)(cyanoethynyl)benzamide.

Synthesised using standard protocol of MnOz oxidation. Reaction time: 45 minutes.

Brown solid, yield: 52%. 1H NMR (400 MHz, METHANOL-d4) 5 7.90 (m, J = 8.50 Hz, 2H), 7.80 (m, J = 8.50 Hz, 2H), 3.42-3.55 (m, 2H), 3.25-3.35 (m, 2H), 2.13-2.23 (m, 2H), 1.92-1.98 (m, 2H); 13C NMR (101 MHz, METHANOL-d4) 5 168.7, 138.8, 134.9, 128.9, 121.4, 105.8, 83.0, 67.3, 41.9, 39.8, 22.8; : C13H12BrN20+ [M+H]+, 291.0; found 291.2. 40: (4-(4-(Cyanoethynyl)benzamido)butyl)tris(2,4,6- trimethoxyphenyl)phosphonium roacetate. 403 (1 eq., 30 mg, 0.103 mmol) and tris(2,4,6-trimethoxyphenyl)phosphane (TMPP, 1 eq., 54.9 mg, 0.103 mmol) were dissolved in dry toluene (2 mL). The obtained solution was left overnight at room temperature. The precipitate was filtered, resolubilised in DMSO, and purified by HPLC to give 40 (35 mg, 0.0409 mmol, 40 %) as a white solid. 1H NMR (400 MHz, METHANOL-d4) 57.75 (d, J= 8.50 Hz, 2H), 7.69 (d, J = 8.50 Hz, 2H), 6.16 (d, J = 4.70 Hz, 2H), 3.76 (s, 9H), 3.51 (s, 18H), 3.35 (t, J = 7.10 Hz, 2H), 2.98-3.10 (m, 2H), 1.53-1.64 (m, 2H); 13C NMR (101 MHz, METHANOL-d4) 5 168.5, 167.5, 165.3, 138.7, 134.9, 128.8, 121.2, 105.8, 94.0, 92.9, 92.3, 82.9, 64.5, 56.5, 41.7, 27.8, 25.7; MS: C40H44N2010P+ [M]+, 728; found 743.23946.

WO 2015001117 60 Compounds 38-40 can be used for detection and/or separation method ing to the invention. 3-(4-(2,5-Dioxo—2,5-dihydro-1H-pyrrolyl)phe-nyl)propiolonitrile (41): o 0&0_ NH2 HN Maleic anhydride TfZO, K2C03 —> —> e DMF I I I I I I N INI INI 7 41a 41 413: (Z)((4-(Cyanoethynyl)phenyl)amino)0X0butenoic acid.

To the solution of 7 (1 eq., 76.8 mg, 0.541 mmol) in acetone (2 mL), maleic anhydride (2 eq., 106 mg, 1.08 mmol) was added. A yellowish solid was obtained after about 7 hours of stirring. The reaction mass was evaporated, an excess of maleic anhydride and maleic acid was washed with methanol. 413 (127 mg, 0.53 mmol, 98 %) was obtained as yellowish solid, no further purification was needed. 1H NMR (400 MHz, DMSO-ds) 8 12.90 (br. s., 1H), 10.70 (s, 1H), 7.62 - 7.90 (m, 4H), 6.50 (d, J: 11.90 Hz, 1H), 6.34 (d, J: 11.90 Hz, 1H); 13C NMR (101 MHz, DMSO-d6) 8 166.8, 163.8, 142.4, 135.0, 131.7, 130.1, 119.3, 110.2, 105.6, 84.3, 61.9; ESI-MS: C13H7N203' [M-H]', 239.0; found 239.0. 41: 2,5-Dioxo-2,5-dihydro-IH-pyrrolyl)phenyl)-propiolonitrile.

To the on of 413 (1 eq., 75 mg, 0.312 mmol) in dry DMF (1.21 mL) trifluoroacetic anhydride (2 eq., 86.9 uL, 0.624 mmol) was added. Stirring continued for another 5 minutes at room temperature and K2C03 (3 eq., 129 mg, 0.937 mmol) was added. The reaction mass stirred for another 60 minutes, then directly purified by HPLC to give 41 (65.9 mg, 0.297 mmol, 95%) as a slightly yellow solid. 1H NMR (400 MHz, DMSO-ds) 5 7.81 (m, J: 8.50 Hz, 2H), 7.52 (m, J: 8.50 Hz, 2H), 6.96 (s, 2H); 13C NMR(101 MHz, DMSO-d6) 8169.0, 134.4, 134.0, 126.0, 117.3, 117.0, 82.2, 78.5, 62.3; ESI-MS: C13H7N202+ [M+H]+, 2230; found 229.9.

Compound 41 can be used for a jugation method according to the invention.

WO 2015001117 61 2014/064387 2,5-Dioxopyrrolidinyl 5-((4-(cyanoethynyl)-phenyl)-amino)0X0pentanoate (42) : 0 O OH I? NH2 flo O NH O NH anhydride DCC, NHS —> _> acetone TEA, DCM N INI INI 42a 42 42a: 5-((4-(Cyanoethynyl)phenyl)amino)0X0pentanoic acid.

To a solution of 7 (1 eq., 200 mg, 1.41 mmol) in acetone (1 mL), glutaric anhydride (2 eq., 321 mg, 2.81 mmol) was added. The obtained solution was stirred for 24 hours at room temperature. Acetone was evaporated, the crude product was recrystallised from IPA-cyclohexane to give 423 (324 mg, 1.27 mmol, 90 %) as a grey solid. 1H NMR (400 MHz, DMSO-ds) 810.21 (s, 1H), 8.15 (br. s., 1H), 7.60 (d, J = 8.72 Hz, 2H), 7.52 (d, J = 8.72 Hz, 2H), .62 (m, 4H), 2.22-2.32 (m, 2H); 13C NMR (101 MHz, DMSO-d6) 8170.0, 168.5, 140.9, 134.2, 119.0, 111.9, 105.4, 84.1, 63.3, 30.1, 29.0, 21.2; ESI-MS: C14H11N203' [M-H]', 255.1; found 255.1. 42: 2,5-Dioxopyrrolidinyl 5-((4-(cyanoethynyl)phenyl)-amino)oxopentanoate.

To a solution of 42a (1 eq., 18 mg, 0.0702 mmol) in DCM (1 mL), DCC (1.02 eq., 14.8 mg, 0.0716 mmol) and TEA (1 eq., 6.52 mg, 5 mL, 0.0644 mmol) were added.

The obtained reaction mass was stirred for 5 minutes, NHS (1 eq., 8.08 mg, 0.0702 mmol) was added. The resulting solution stirred for another 2 hours at room temperature. The crude product was purified by flash chromatography (cyclohexane- EtOAc) to give 42 (6.45 mg, 0.0183 mmol, 26%) as a white solid. 1H NMR (400 MHz, CHLOROFORM-d) 8 8.27 (br. s., 1H), 7.64 (d, J = 8.78 Hz, 2H), 7.57 (d, J = 8.78 Hz, 2H), 2.94 (s, 4H), 2.74 (t, J = 6.53 Hz, 2H), 2.52 (t, J = 6.90 Hz, 2H), 2.23 (m, 2H); 13C NMR (101 MHz, CHLOROFORM-d) d 170.3, 169.5, 168.2, 141.3, 134.6, 119.4, 112.4, 105.7, 83.2, 62.9, 35.6, 29.9, 25.7, 21.2; ESI—MS: C18H16N305+ [M+H]+, 353.1; found 353.2.

Compound 42 can be used for a bioconjugation method according to the invention.

WO 2015001117 62 3-(4-azidophenyl)propiolonitrile (43): HZN : _N |AN,TMSN3 N :N —————> ,3 K2C03'ACN _// 7 (1 eq., 151 mg, 1.07 mmol) was dissolved in acetonitrile (2.34 mL) in a 25 mL roundbottomed flask and cooled to 0°C in an ice bath. To this stirred mixture was added isoamyl nitrite (IAN, 1.5 eq., 215 uL, 1.6 mmol) followed by trimethylsilyl azide (1.2 eq., 147 mg, 0.168 mL, 1.28 mmol) dropwise. The resulting solution was stirred at room ature for 45 minutes. The reaction mixture was concentrated under vacuum and the crude product was resolubilised in EtOAc, washed with water, dried and ated to give 43 (177 mg, 1.06 mmol, 99%). 1H NMR (400 MHz, ACETONITRILE-ds) 6 7.58 = 8.78 Hz, 2H), 7.11 — 7.81 (m, J - 7.26 (m, J = 8.78 Hz, 2H); 13C NMR (101 MHz, ACETONITRILE-ds) 5 144.9, 136.0, 120.4, 113.6, 105.9, 83.4, 62.9; GC-ESI-MS: C9H5N4+ [M+H]+, 169.0; found 169.0.

S-Azido-N-(4-(cyanoethynyl)phenyl)pentanamide (44): NH2 HN CIJ‘J\/\/\N3 44a N3 ll M 44a: opentanoyl chloride. opentanoic acid (1 eq., 1.1 g, 6.99 mmol) was refluxed in SOClz (10 eq., 5.1 mL, 69.9 mmol) for 30 minutes. Excess of SOClz was removed in vacuo and the obtained crude solid was used in the next step without purification. 44: S-Azido-N-(4-(cyanoethynyl)phenyl)pentanamide. 7 (1 eq., 16.1 mg, 0.113 mmol) and TEA (1.5 eq., 24 uL, 0.17 mmol) were dissolved in DCM (3 mL), cooled to -78 °C, and 443 (1.1 eq., 20.1 mg, 0.125 mmol) was added to the reaction mixture that was then left to warm to room temperature while stirring for another 1 hour. The reaction mass was washed with 1M HCl (2x1 mL), water (2 mL), WO 2015001117 63 2014/064387 dried over Na2S04, and evaporated to give crude product, which was purified by flash chromatography to give 44 (25.5 mg, 0.101 mmol, 89 %) as a grey solid. 1H NMR (400 MHz, METHANOL-d4) 8 7.58 = 8.70 Hz, 2H), 7.40 - 7.67 (m, J - 7.58 (m, J: 8.70 Hz, 2H), 3.23 - 3.28 (m, 2H), 2.34 (t, J: 7.28 Hz, 2H), 1.61 - 1.72 (m, 2H), 1.49 - 1.61 (m, 2H); 13C NMR (101 MHz, METHANOL-d4) 8173.0, 144.0, 135.7, 134.3, 120.7, 113.0, 106.2, 84.5, 40.4, 34.4, 28.8, 24.0; ESI-MS: C14H14NsO+ [M+H]+, 2681; found 268.1. 1-[4-(Cyanoethynyl)benzyl]-3,3,6,6-tetramethyl-4,5-didehydr0-2,3,6,7- tetrahydrothiepinium triflate (45): propargylic alcoholCul PPha) MnOz NHa NBS DIPEA, DMF \\ \ —’ MgSO4 IPA THF \ MW,CC|4 ‘OTf BI’ I l 8+ TMTH LiOTf, DCM/HZO \\ \\ N \\ 45a 45 45c: 3-(p-Tolyl)prop-2—ynol. sised using protocol A for Sonogashira coupling. Yellowish solid, yield: 88%. 1H NMR (400 MHz, ACETONITRILE-ds) 6 7.25 = 8.03 Hz, 2H), 7.04 - 7.49 (m, J - 7.25 (m, J = 8.03 Hz, 2H), 4.34 (d, J: 6.02 Hz, 2H), 3.31 (t, J = 6.02 Hz, 1H), 2.32 (s, 3H); 13C NMR (101 MHz, ACETONITRILE-dg) 8139.8, 132.4, 130.3, 120.8, 88.8, 85.1, 51.2, 21.5; : C10H110+ [M+H]+, 146.1; found 146.0. 45b: 3-(p-Tolyl)propiolonitrile.

The compound was obtained as the only product of the standard MnOz oxidation protocol. Reaction time: 3 hours. White solid, yield: 67%. 1H NMR (400 MHz, METHANOL-d4) 87.37 = 8.03 Hz, 2H), 7.02 - 7.59 (m, J - 7.31 (m, J= 8.03 Hz, 2H), 2.29 (s, 3H); 13C NMR (101 MHz, METHANOL-d4) 143.2, WO 2015001117 64 2014/064387 133.3, 129.5, 114.0, 104.8, 83.2, 61.3, 20.4; ESI-MS: C10H8N+[M+H]+, 141.1; found 141.0. 453: 3-(4-(Bromomethyl)phenyl)propiolonitrile.

Degased solution of 45b (1 eq., 68 mg, 0.482 mmol) in DCM (1 mL) was MW- irradiated (100°C) for 5 minutes. The reaction e was evaporated, the crude was purified by preparative HPLC to give 453 (42.4 mg, 0.193 mmol, 40 %) as a yellowish solid. 1H NMR (400 MHz, CHLOROFORM-d) 5 7.56 - 7.71 (m, J = 8.28 Hz, 2H), 7.40 - 7.49 (m, J = 8.28 Hz, 2H), 4.48 (s, 2H); 13C NMR (101 MHz, CHLOROFORM-d) 141.8, 133.9, 129.5, 117.5, 105.3, 82.3, 63.7, 31.8; -MS: C10H7BrN+ [M+H]+, 219.0; found 219.0. 45: 1-[4-(Cyanoethynyl)benzyl]-3,3,6,6-tetramethyl-4,5-didehydro-2,3,6,7- tetrahydrothiepinium triflate.

To a degassed solution of 453 (1 eq., 43.7 mg, 0.199 mmol) and TMTH (1.29 eq., 43 mg, 0.255 mmol; synthesised following previously described procedures“) in DCM (1.34 mL), a on of LiOTf (11.6 eq., 360 mg, 2.31 mmol) in distilled and degased H20 (0.668 mL) was added. The obtained biphasic mixture was vigorously stirred for days at 25 °C (degasing once per day). Two phases were separated, the organic one was washed with DCM (5X2 mL). United organic fractions were ated and the crude was purified by HPLC to give 45 (46.9 mg, 0.111 mmol, 56 %) as colourless oil (crystallizes slowly at 0 °C to yield a white solid). 1H NMR (400 MHz, CHLOROFORM-d) 57.65 = 8.03 Hz, 2H), 7.56 - 7.73 (m, J - 7.65 (m, J = 8.03 Hz, 2H), 5.07 (s, 2H), 4.12 (d, J = 12.30 Hz, 2H), 3.72 (d, J = 12.30 Hz, 2H), 1.36 (s, 6H), 1.30 (s, 6H); 13C NMR (101 MHz, DMSO-d6) 8135.1, 133.6, 131.9, 117.8, 106.4, 105.8, 83.3, 63.6, 60.1, 43.2, 34.6, 26.4, 25.4; HR-ESI-MS: C20H22NS+ [M]+, 308.1; found 308.1.

Compounds 43-45 can be used for a click chemistry (such as reaction click - azide) according to the invention. nd 45 can be used for strain promoted click according to the invention.

W0 20151001117 65 1 - ({4 - [1 - {[2 - ({3 - Carboxylato [6 - (dimethylamino) (dimethyliminiumyl) - 3H — xanthen - henyl}formamido)ethyl]sulfanyl} — 2 - cyanoeth — 1 - en yl]phenyl}methyl) - 3,3,6,6 - tetramethyl - 1 — thiacyclohept yn ium trifluoroacetate (46): TFA' 8+ I I I I ACN, DIPEA 46a: Dimethylamin0)(dimethyliminio)-3H-Xanthenyl)((2-mercaptoeth yl)carbam0yl)benzoate.

To a solution of TAMRA-5’-COOH (1 eq., 68.3 mg, 0.159 mmol) in DMF (0.228 mL), HATU (1 eq., 60.3 mg, 0.159 mmol), DIPEA (6 eq., 123 mg, 0.157 mL, 0.952 mmol) and cystamine dichloride (5 eq., 178 mg, 0.793 mmol) were subsequently added; the obtained solution mass was d overnight. A solution of DTT (5 eq., 122 mg, 0.118 mL, 0.793 mmol) in DCM (0.911 mL) was added to the reaction mass, the stirring continued for 2 hours. Solvents were evaporated; the obtained crude mass was purified by HPLC to yield 463 (33.5 mg, 0.0555 mmol, 35 %) as a dark-Violet solid. 1H NMR (400 MHz, DMSO-ds) 89.06 (t, J = 5.4 Hz, 1H, 8.70 (d, J = 1.8 Hz, 1H), 8.30 (dd, J = 1.8, 8.0 Hz, 1H), 7.59 (d, J = 8.0 Hz, 1H), 7.08-7.02 (m, 4H), 6.95 (s, 2H), 3.52-3.42 (m, 2H), 3.26 (s, 12H), 2.72 (dt, J = 6.8, 8.0 Hz, 2H); 13C NMR (101 MHz, DMSO-d6) 8166.0, 164.7, 156.8, 156.6, 135.9, 131.2, 130.6, 114.6, 96.3, 42.9, 40.5, 23.3; -MS: C27H27N3O4S: 489.1722; found 489.1723. 46: 1-({4-[(1Z){[2-({3-Carboxylato-4—[6-(dimethylamino)-3— (dimethyliminiumyl)-3H-xanthenyl]phenyl}formamido)ethyl]sulfanyl} cyanoeth-l-enyl]phenyl}methyl)-3,3,6,6—tetramethylthiacycloheptynium trifluoroacetate (TAMRA-APN-TMTI).

WO 2015001117 66 A solution of 45 (1 eq., 6.74 mg, 0.016 mmol) in ACN (1 mL) was mixed with a solution of 46a (1 eq., 9.64 mg, 0.016 mmol) in DMF (1 mL). DIPEA (5 eq., 132 uL, 0.08 mmol) was then added and obtained reaction mass was injected into HPLC after 5 s of reaction to yield 46 (11.9 mg, 0.0149 mmol, 93 %) as a dark-violet solid. 1H NMR (400 MHz, DMSO—ds) 88.98 (t, J = 5.40 Hz, 1H), 8.30 (d, J = 8.28 Hz, 1H), 8.10 - 8.20 (m, 1H), 7.85 (s, 1H), 7.57 - 7.69 (m, 4H), 6.97 - 7.15 (m, 5H), 6.07 (s, 1H), 4.85 (s, 2H), 2.81 - 2.90 (m, 4H), 3.28 (br. s., 16H), 1.25 (s, 6H), 1.05 (s, 6H); 13C NMR (101 MHz, DMSO-d6) — not ative (low resolved signals); HR-ESI-MS: C47H49N4O4S2+, 797.31897; found 797.32739. 1 - ({4 — [2 - Cyano — 1 - [(2 — {4 - [(E) - 2 — [4-(dimethylamino)phenyl]diazen — 1 - yl]benzenesulfonamido}ethyl)sulfanyl]eth en-l - yl]phenyl}methyl) - 3,3,6,6 - tetramethyl thiacyclohept — 4 - yn — 1 - ium (47, BHQZ-APN- TMTI): TfO \\ 3+ <j // TFA N SH N” HN—g N O \‘o/N N l | \ 47a 0=S=O N\\ / rim INI ACN, DIPEA s/\/ 47a: (E)((4-(Dimethylamino)phenyl)diazenyl)-N- captoethyl)benzenesulfonamide.

To a cooled to 0°C solution of Dabsyl chloride (1 eq., 100 mg, 0.309 mmol) in dry ACN (3 mL), TEA (7 eq., 218 mg, 0.3 mL, 2.16 mmol) and cystamine dihydrochloride (5 eq., 347 mg, 1.54 mmol) were subsequently added. After 2 hours of stirring, DTT (6 eq., 285 mg, 0.275 mL, 1.85 mmol) was added to the reaction mass. The obtained solution was stirred for another 2 hours, evaporated and the obtained crude product was purified by flash chromatography (cyclohexane-EtOAc) to yield 473 (105.9 mg, 94%) as an orange solid.

W0 20151001117 67 47: 1-({4-[(2-Cyano[(2-{4-[(E)[4- (dimethylamino)phenyl]diazen yl]benzenesulfonamido}ethyl)sulfanyl]eth-l-en nyl}methyl)-3,3,6,6-tetramethyl thiacyclohept—4—ynium trifluoroacetate.

The same ure as for the synthesis of the 46. Yield: 94%. 1H NMR (400 MHz, DMSO—ds) 58.03 (t, J = 4.89 Hz, 1H), 7.91 (d, J = 8.53 Hz, 2H), 7.80 - 7.87 (m, J: 9.04 Hz, 2H), 7.72 - 7.79 (m, J: 8.53 Hz, 2H), 7.68 (s, 4H), 6.87 (d, J = 9.04 Hz, 2H), 6.08 (s, 1H), 4.86 (s, 2H), 3.92 (d, J = 12.05 Hz, 2H), 3.84 (d, J = 12.30 Hz, 2H), 3.10 (s, 6H), 2.71 - 2.87 (m, 4H), 1.32 (s, 6H), 1.17 (s, 6H); 13C NMR (101 MHz, DMSO-ds) 5160.2, 158.6, 158.3, 155.1, 153.7, 143.1, 140.3, 136.8, 131.9, 131.3, 129.5, 128.2, 125.9, 122.8, 117.2, 112.1, 106.4, 99.4, 60.0, 43.3, 42.9, 34.5, 26.4, .3; HR—ESI-MS: C36H42N50283+, 672.24951; found 672.25042.

Compounds 46-47 can be used for the preparation of compounds otherwise not accessible (TMTI).

WO 1117 68 -(3—{4—[1-(4 - {[4 - (2 - Cyanoeth-l - yn yl)phenyl]carbamoyl}butyl) - 1H - 1,2,3 — triazol - 4-yl]butanamido}propyl) — 2 - [(E) - 2 — [4 - y — 2 - (2 — {2 - [2 - (2 - {5 - [(4S) 0X0 - hexahydro - 1H - thieno[3,4 - d]imidazolidin - entanamido}ethoxy)ethoxy]ethoxy}ethoxy)phenyl]diazen yl]benzoic (48, APN-HAZA-biotin): OH 01(1ng/,NN goA/OI o 44, CuSO4-5H20 sodium ascorbate O —’ 1 NH DMSOIHZO NH O \\ O \\ / IIN “I“ s | | ML? ‘71/NH HN O 0 48a 48 Compound 48 can be used for purification and/or immobilization according to the invention. 4821: 2-(6-(Dimethylamino)(dimethyliminio)-3H-Xanthenyl)((2-mercaptoeth yl)carbamoyl)benzoate.

This compound was synthesised following the previously reported protocol. 48: 5-(3—{4—[1-(4—{[4-(2-Cyanoethynyl)phenyl]carbamoyl}butyl)-1H—1,2,3— triazolyl]butanamido}propyl)[(E)[4-hydroxy(2-{2-[2-(2-{5-[(4S)oxo- hexahydro-1H-thieno[3,4-d]imidazolidin WO 2015001117 69 tanamido}ethoxy)eth0xy]ethoxy}ethoxy)phenyl]diazenyl]benzoic (APN- HAZA-biotin).

To a solution of 483 (1 eq., 10 mg, 0.0123 mmol) and 77 (1 eq., 3.12 mg, 0.0123 mmol) in DMSO (0.472 mL), solution of sodium ascorbate (10 eq., 24.4 mg, 0.123 mmol) and CuSO4'5H20 (5 eq., 15.4 mg, 0.0617 mmol) in water was added. The obtained reaction mass was degassed and stirred overnight at 25 °C. The reaction mass was directly purified by HPLC to give 48 (8.3 mg, 0.0078 mmol, 63 %) as a yellow solid. 1H NMR (400 MHz, METHANOL—d4) 57.78 (br. s., 2H), 7.72 (d, J = 8.28 Hz, 1H), 7.67 (s, 1H), 7.58 (d, J = 8.78 Hz, 2H), 7.50 (d, J = 8.78 Hz, 2H), 7.29 (d, J = 8.28 Hz, 1H), 7.25 (d, J: 8.53 Hz, 1H), 6.29 (d, J: 7.78 Hz, 1H), 3.70 - 3.81 (m, 8H), 3.62 (d, J = 4.77 Hz, 2H), 3.58 (d, J: 5.02 Hz, 2H), 3.48 - 3.53 (m, 2H), 3.41 - 3.48 (m, 2H), 3.01 - 3.07 (m, 6H), 2.89 - 3.00 (m, 10H), 2.78 (dd, J: 4.89, 12.93 Hz, 1H), 2.52 - 2.67 (m, 8H), 2.33 (t, J: 7.28 Hz, 2H), 2.09 - 2.19 (m, 2H), 1.81 - 1.91 (m, 4H), 1.65 - 1.78 (m, 2H), 1.52 - 1.63 (m, 2H), 1.42 - 1.52 (m, 1H), 1.23 - 1.31 (m, 1H); HR-ESI—MS: N110iiS, 1077.47422; found 1077.45931. 2-((4-(cyanoethynyl)phenyl)amino)-N,N,N-trimethyloxoethan-l-aminium trifluoroacetate (49): o N+\ >_/ / O \N‘ CI' \ N— — NH2 —> N: : NH DIPEA, DMF TFA. 7 49 49a: 2-chl0r0-N,N,N-trimethyl-Z-oxoethan-I-aminium.

Synthesised as previously described by Vassel and Skelly (10.1002/0471264180.os035.09). 49: 2-((4-(cyanoethynyl)phenyl)amino)-N,N,N-trimethyloxoethan-l-aminium trifluoroacetate.

To a on of 3-(4-aminopheny1)propynenitrile (1 eq., 66.3 mg, 0.466 mmol) and DIPEA (1.1 eq., 66.3 mg, 0.0848 mL, 0.513 mmol) in DMF (1 mL), a cooled to -20 “C solution of (2-chlorooxoethyl)trimethy1azanium chloride (1.1 eq., 88.3 mg, 0.513 mmol) in DMF (1 mL) was added. The obtained reaction mass was stirred at 25 °C for W0 20151001117 70 hours, purified by RP-flash chromatography to give 49 as a yellowish solid (39 mg, 0.110 mmol, 24%). 1H NMR (400 MHz, ACETONITRILE-ds) 811.14 (br. s., 1H), 7.70 = 8.78 - 7.83 (m, J Hz, 2H), 7.56 = 8.78 Hz, 2H), 4.33 - 7.70 (m, J (s, 2H), 3.28 (s, 9H); 13C NMR (101 MHz, ACETONITRILE-ds) 8163.5, 142.5, 135.8, 121.2, 113.5, 106.5, 84.4, 66.3, 63.1, 55.2; ESI-MS: C14H16N30+ [M]+, 242.13; found 242.13. 1-(4-(cyanoethynyl)phenyl)-1H-1,2,3-triazolyl)-2,5,8,11,14- pentaoxaheptadecanamid0)pentanedioic acid (50): _ _ N: \ N_ _ N —> \ \ /\ /\/0\/\o o N 0 OH A on of 43 (1 eq., 5.65 mg, 0.0336 mmol) in DMSO (0.0331 mL), a solution of di- acid-alkyne (1 eq., 14.6 mg, 0.0336 mmol) in water (0.0331 mL) was added. A solution of copper sulfate pentahydrate (0.1 eq., 0.839 mg, 0.00336 mmol) in minimum t of water was added to the obtained reaction mass followed by the addition of a solution of sodium ascorbate (0.5 eq., 3.33 mg, 0.0168 mmol) in minimum ammount of water. The addition repeated after 30 minutes until complete dissapearance of the strasting material (2 times overall). Excess of water was evaporated to vacuo (no heating should be used, otherwise hydrolysis product starts to appear), the obtained crude mass was d by HPLC after the filtration of copper salts through a seringe filter to give 50 (11 mg, 0.01828 mmol, 54%) as a white solid. 1H NMR (400 MHz, ACETONITRILE-dg) 88.41 (s, 1H), 7.95 - 8.02 (m, 2H), 7.88 - 7.94 (m, 2H), 6.86 (d, J = 7.78 Hz, 1H), 4.71 (s, 2H), 4.49 (td, J = 6.71, 8.41 Hz, 1H), 3.68 = 2.42, 4.96 - 3.76 (m, 3H), 3.49 - 3.68 (m, 21H), 2.53 - 2.64 (m, 5H), 1.97 (td, J Hz, 15H); 13C NMR (101 MHz, ACETONITRILE-ds) 8188.7, 173.3, 161.6, 146.5, 135.1, 131.3, 130.8, 122.5, 121.0, 117.9, 115.4, 64.2, 40.4, 39.5, 36.7, 30.6; : C28H34N5010‘ [M-H]‘, 600.21; found 600.23.

W0 20151001117 71 N1,NS-bis(23-amino-3,6,9,12,15,18,21-heptaoxatricosyl)(1-(1-(4- ethynyl)phenyl)-1H-1,2,3-triazolyl)-2,5,8,11,14- pentaoxaheptadecanamido)pentanediamide (51): NEG—N3 —> 0%HN ”NOWO/VOV\O/\/o\/\O/\/o\/\NH2 jgO 43 51 A solution of 43 (1 eq., 1.64 mg, 0.00973 mmol) and PEG-Alkyne (1 eq., 11 mg, 0.00973 mmol) in DMSO was added to a mixture of DMSO (0.00958 mL) and water (0.00958 mL). A solution of copper sulfate pentahydrate (0.1 eq., 0.243 mg, 0.000973 mmol) in minimum ammount of water was added to the obtained on mass followed by the addition of a solution of sodium ascorbate (0.5 eq., 0.964 mg, 0.00487 W0 20151001117 72 mmol) in minimum ammount of water. The reaction mass was filtered and purified by HPLC to give 51 (5 mg, 0.003839 mmol, 39%) as a colorless liquid.

MS: C60H103N9022, 2177; found 1301.72204.

N-(17-amino-3,6,9,12,15-pentaoxaheptadecyl)(1-(4-(cyanoethynyl)phenyl)- 1H-1,2,3-triazolyl)-2,5,8,11,14-pentaoxaheptadecanamide (52): H2N\L ”N o N\N\ N;QN3 N —’ NWWOV\ONOV\O/\/O\j A on of 3-(4-azidophenyl)propynenitrile (1 eq., 14.9 mg, 0.0886 mmol) in DMSO (0.0872 mL), a solution of PEG-alkyne (1 eq., 50.2 mg, 0.0886 mmol) in water (0.0872 mL). To the obtained mixture a solution of copper sulfate ydrate (0.1 eq., 2.21 mg, 0.00886 mmol) in minimum ammount of water was added followed by the addition of a solution of sodium ascorbate (0.5 eq., 8.77 mg, 0.0443 mmol) in minimum ammount of water. The addition of copper sulfate pentahydrate (0.1 eq., 2.21 mg, 0.00886 mmol) and sodium ascorbate (0.5 eq., 8.77 mg, 0.0443 mmol) were repeated after 30 minutes if starting azide was still present. Excess of water was evaported to vacuo, the crude product was purified by HPLC to give 52 (55 mg, 0.07485 mmol, 84%) as a colorless oil. 1H NMR (400 MHz, ACETONITRILE-ds) 88.42 (s, 1H), 7.95 = 9.03 Hz, - 8.02 (m, J 2H), 7.86 - 7.95 (m, J: 8.78 Hz, 2H), 7.30 (br. s., 2H), 7.19 (br. s., 1H), 4.71 (s, 2H), 3.73 - 3.79 (m, 2H), 3.65 - 3.73 (m, 7H), 3.54 - 3.65 (m, 29H), 3.51 (t, J: 5.40 Hz, 2H), 3.34 (q, J= 5.35 Hz, 2H), 3.13 (d, J: 4.52 Hz, 2H), 2.37 - 2.46 (m, 2H), 1.92 - 2.01 (m, 5H); 13C NMR (126 MHz, FORM-d) 8177.5, 151.3, 144.6, 140.7, 140.7, W0 20151001117 73 140.6, 127.2, 126.0, 125.9, 125.8, 122.4, 110.5, 87.2, 75.4, 75.3, 75.3, 75.2, 75.2, 75.1, 75.1, 75.1, 75.0, 74.9, 74.8, 74.8, 72.2, 71.9, 68.9, 68.5, 45.0, 44.2, 41.6; ESI-MS: C35H55N6011+ , 735.39; found 735.20. 1-(4-(cyan0ethynyl)phenyl)(3-(dimethylamino)propyl)urea (53): CI 0 CI C'>k JL x0 CI 0 0 CI //N I TEA / HN N —’ 2 : :N W + W \ THF,r.t.,2hours \NMNJLN I H H 7 53 To a solution of triphosgene (1 eq., 56.3 mg, 31.6 uL, 0.19 mmol) in THF (0.404 uL) was added a solution of 3-(4- aminopheny1)propynenitrile (3 eq., 80.9 mg, 0.569 mmol) in THF (0.404 uL). Then triethylamine (6 eq., 115 mg, 158 uL, 1.14 mmol). The e was stirred for 5 min and then 3-dimethylaminopropylamine (3 eq., 58.1 mg, 71.8 uL, 0.569 mmol) and triethylamine (2 eq., 38.4 mg, 52.7 uL, 0.379 mmol) was added in THF (0.404 uL). The reaction mixture was stirred for 10 minutes and then concentrated. The obtained residue was purified by HPLC to give 53 (47 mg, 0.1764 mmol, 93%) as a white solid. 1H NMR (400 MHz, METHANOL-d4) 87.45 - 7.50 (m, 2H), 7.41 - 7.45 (m, 2H), 3.23 - 3.25 (m, 1H), 3.04 - 3.11 (m, 2H), 2.80 (s, 6H), 1.77 - 1.91 (m, 2H); 13C NMR (101 MHz, METHANOL-d4) 8156.5, 143.7, 134.4, 118.0, 109.3, 105.0, 83.7, 61.0, 55.2, 42.1, 35.9, 25.3; ESI-MS: C15H20N4O+ [M+H]+, ; found 271.15. 3-((3-(3-(4-(cyanoethynyl)phenyl)ureid0)propyl)dimethylammonio)propane sulfonate (54): N\\ N\\ \\ 1,3-propanesultone, \\ o Ncho3 o NJLNMN/—> o IPA, 80 00. 3 hours N N/\/\N+’\/\s’/ H H | _ 53 54 53 (1 eq., 27 mg, 0.0702 mmol) and 1,3-propanesultone (1.1 eq., 9.44 mg, 0.00678 mL, 0.0773 mmol) were dissolved in IPA (0.5 mL) and refluxed for 3 h. The reaction mixture was cooled to room ature and the precipitate was filtered and washed WO 01117 74 with cold distilled water to remove any unreacted propanesultone to give 54 (27 mg, 0.0688 mmol, 98 %) as a white solid. 1H NMR (400 MHz, DEUTERIUM OXIDE) 57.45 - 7.67 (m, 2H), 7.33 (br. s., 2H), 3.61 (br. s., 4H), 3.53 (br. s., 1H), 3.39 (br. 5., 2H), 3.31 (br. s., 2H), 3.25 (br. s., 2H), 3.03 (br. s., 7H), 2.89 (br. s., 7H), 2.13 (br. s., 1H), 1.89 (br. s., 7H), 1.08 (br. s., 2H); ESI-HRMS: C18H24N404S, 392.15183; found 392.15254.Compounds 49-54 can be used for a ation method according to the invention, for instance for changing ADME parameters (solubilizing agents). 3-(4-(4-(hydroxymethyl)-1H-1,2,3-triazolyl)phenyl)propiolonitrile (55): sodium ascorbate,Cu| HO/\|%\ _ _ N3 _— :N N _ _N N: / water, THF, 25 “C, 2 hours N 43 55 3-(4-azidophenyl)propynenitrile (1 eq., 300 mg, 1.78 mmol) , 2-propynol (2 eq., 200 mg, 0.211 mL, 3.57 mmol) were solubilized in THF (9 mL). To this mixture was added a solution of copper e pentahydrate (10 %, 44.5 mg, 0.178 mmol) in 1.5 mL of water followed by the solution of sodium ascorbate (0.5 eq., 176 mg, 0.892 mmol) in 1.5 mL of water. The ing solution was stirred for 2h and then concentrated on rotary evaporator. The residue was extracted with DCM. The organic layer was washed with NH4C1 (sat) and water, dried over MgSO4 and then evaporated. The residue was resolubilised in DCM and the product was filtered to give 55 (23.28 mg, 8 mmol, 92%) as a slightly yellowish solid. 1H NMR (400 MHz, MeOD) 8 8.58 (s, 1H), 8.04 (d, J = 7.4 Hz, 2H), 7.93 (d, J = 7.4 Hz, 2H), 4.77 (s, 2H); ESI-MS: C12H9N4O+ , 225.08; found 225.05. 3-(4-(4-(bromomethyl)-1H-1,2,3-triazolyl)phenyl)propiolonitrile (56): HOyr: PBr3 : :N Br/Y\N : :N NQN’ THF, 25 00, 15 hours NQN 55 56 55 (1 eq., 19.8 mg, 0.0881 mmol) was dissolved in THF (1 mL) under nitrogen at room temperature and 3-{4-[4-(bromomethyl)—1H-1,2,3-triazolyl]phenyl}prop ynenitrile (23.3 mg, 0.0811 mmol, 92 %) was added. The reaction mixture was stirred at room WO 2015001117 75 ature for 15 hours. ts were evaporated, the crude product was purified by HPLC to give 56 (23.3 mg, 0.0811 mmol, 92 %) as a white solid. 1H NMR (400 MHz, ACETONITRILE-ds) 88.44 (s, 1H), 7.78 - 8.03 (m, 5H), 4.74 (s, 2H); 13C NMR (101 MHz, CHLOROFORM-d) 8150.9, 144.3, 140.6, 140.5, 126.0, 125.9, 110.4, 87.1, 68.5, 27.0; ESI-MS: C12H8BrN4+ [M+H]+, 286.99; found 287.08.

Compound 56 can be used for a bioconjugation method according to the invention. 1-({1-[4-(cyanoethynyl)phenyl]-1H-1,2,3-triazolyl}methyl)-3,3,6,6-tetramethyl- 4,5-didehydro-2,3,6,7-tetrahydrothiepinium trifluoroacetate (57): F 3 Br/\F\ TMTH, LIOTf. 3+ N _— :N \\ N — _N NQN’ DCM, water, 25 "C, 150 hours 56 57 To a degassed solution of 4-(bromomethyl)-1H—1,2,3-triazol-l-yl]phenyl}prop ynenitrile (1 eq., 19.6 mg, 0.0684 mmol) and TMTH (1.89 eq., 21.7 mg, 0.129 mmol) in DCM (0.982 mL), a solution of lithium triflate (10 eq., 106 mg, 0.684 mmol) in water (0.982 mL) was added. The obtained biphasic mixture was usly mixed for 2 days at 25 ”C. Phases were separated, organic phase was washed with DCM (5x2 mL).

United organic fractions were evaporated and the crude was purified by HPLC to give 57 (23.7 mg, , 66%) as a white solid.

ESI-HRMS: C22H23N4S, 375.16434; found 375. 16497.

Compound 57 can be used for click-chemistry (strain promoted click) according to the invention. 4-(((1-(4-(cyanoethynyl)phenyl)-1H-1,2,3-triazol-4—yl)methyl)carbamoyl)(6- (dimethylamino)-3—(dimethyliminio)-3H-xanthenyl)benzoate (58): WO 01117 76 N‘ ‘ AFN-NB, sodium ascorbate, Cul THF/H20, 25 °C, 30 mins 2-[6-(dimethylamino)—3-(dimethyliminiumyl)—3H-xantheny1]-4—[(propyn yl)carbamoyl]benzoate (1 eq., 52.8 mg, 0.113 mmol) and 3-(4-azidophenyl)prop ynenitrile (1 eq., 19 mg, 0.113 mmol) were solubilized in THF (1 mL). H20 (1 mL) was added to the obtained reaction mixture followed by the addition of solutions of Copper Sulphate pentahydrate (10 %, 2.82 mg, 0.0113 mmol) and sodium ascorbate (50 %, 11.2 mg, 0.0565 mmol) in minimum amount of water (separately). The ed reaction mixture was stirred for r 30 minutes, evaporated and purified by HPLC to give 58 (66.8 mg, 0.105 mmol, 93 %) as a dark-violet solid. 1H NMR (400 MHz, METHANOL-d4) 88.51 (s, 1H), 8.33 (d, J = 8.28 Hz, 1H), 8.16 (dd, J = 1.51, 8.28 Hz, 1H), 7.86 — 8.02 (m, 2H), 7.64 - 7.86 (m, 3H), 7.02 - 7.12 (m, 2H), 6.84 - 7.02 (m, 4H), 4.58 - 4.71 (m, 2H); ESI-HRMS: C37H29N7O4, 635.22811; found 635.22861. 3-(9-(diethylamino)0X0-5H-benzo[a]phenoxazinyl)propiolonitrile (59): OH O\\ J<F S F O \O\ propargylic alcohol, TEA’ TfCI L11 9N O DIPEA, PdCI2(PPh3)2 N —> N O O L 2 hours K N O O OH N N O MnOz‘ MgSO4, NH, L \ —, N\ THF, 25 00, 15 mins N o 0 L Q: Q K NK 0 0 59a 59 WO 20151001117 77 59b: 8-(diethylamino)—3-hydroxy-12Hoxaazatetraphenone (1 eq., 65 mg, 0.194 mmol) was dissolved in dry DCM (2 mL) and cooled to 5 °C. Then TEA (1.2 eq., 23.6 mg, 0.0324 mL, 0.233 mmol) was added followed by the addition of TfCl (1.2 eq., 39.3 mg, 0.0249 mL, 0.233 mmol). The addition of Tf20 was repeated untile complete disappearance of the starting material. The solvent was evaporated and the residue was treated with water. The precipitate was filtered off and washed with water and heptane to give the desired product (76 mg, 0.163 mmol, 84 %) as a iolet solid.

ESI-HRMS: C21H17F3N205S, 466.08103; found 466.08221. 593: Under an inert atmosphere, DIPEA (2 eq., 16.1 mg, 0.0206 mL, 0.124 mmol) and Propargylic alcohol (1.5 eq., 5.23 mg, 0.00551 mL, 0.0933 mmol) were added to a on of 59b (1 eq., 29 mg, 0.0622 mmol), PdC12(PPh3)2 (5 %, 2.18 mg, 0.00311 mmol) and CuI (10 %, 1.18 mg, 0.00622 mmol) in DMF (1 mL). After stirring for 2 hours at 90 °C, the solvent was removed under reduced pressure. The crude product was purified by flash chromatography (DCM-MeOH from 100-0 to 80- 20).

ESI-HRMS: C23H20N203, 372.14739; found 372.14735. 59: To the solution of 59a (1 eq., 10 mg, 0.0269 mmol) in THF (0.121 mL) was added MgSO4 (15 eq., 48.5 mg, 0.403 mmol), NH3 (4 eq., 2 M, 0.0537 mL, 0.107 mmol), and Mn02 (15 eq., 35 mg, 0.403 The reaction mixture was d at r.t. for 15 mins and followed by HPLC. After completion the mixture was filtered h Celite and washed thoroughly with THF. Evaporation of the filtrate gave crude 59 (9.47 mg, 0.0258 mmol, 96 %) which was purified by HPLC. 1H NMR (400 MHz, CHLOROFORM—d) 88.91 (s, 1H), 8.26 (d, J = 8.03 Hz, 1H), 7.79 (dd, J: 1.51, 8.03 Hz, 1H), 7.62 (d, J: 9.29 Hz, 1H), 6.74 (dd, J: 2.63, 9.16 Hz, 1H), 6.51 (d, J = 2.51 Hz, 1H), 6.35 (s, 1H), 5.31 (s, 2H), 3.49 (q, J = 7.11 Hz, 4H), 1.09 - 1.36 (m, 6H); ESI-HRMS: C23H17N302, 367.13208; found 367.13145.

(E)(4-((4-(dimethylamino)phenyl)diazenyl)phenyl)propiolonitrile (60): H N : :N —> z 2 ’ N: — N \ 7 60 7 (1 eq., 167 mg, 1.17 mmol) was ved in acetonitrile (2.58 mL). To this stirred mixture was added l nitrite (1.5 eq., 206 mg, 0.237 mL, 1.76 mmol), stirring W0 20151001117 78 continued for another 2 minutes, then dimethylaniline (1.1 eq., 156 mg, 0.165 mL, 1.29 mmol) was added. The ing reaction mixture was stirred overnight (turned red), evaporated and purified by flash chromatography (DCM, first peak) to give 60 (120 mg, 0.437 mmol, 37 %) as red solid. 1H NMR (400 MHz, CHLOROFORM-d) 57.91 (d, J = 9.03 Hz, 2H), 7.82 = - 7.88 (m, J 8.53 Hz, 2H), 7.62 = 8.53 Hz, 2H), 6.77 (d, J = 9.03 Hz, 2H), 3.08 - 7.77 (m, J - 3.18 (m, 6H); 13C NMR (101 MHz, CHLOROFORM-d) 5154.7, 153.2, 143.7, 134.4, 125.8, 122.5, 117.3, 111.6, 105.6, 83.3, 64.2, 40.3; ESI-HRMS: C17H14N4, 274.12185; found 274.12247. nds 58-60 can be used for a detection method method according to the invention. tert-butyl ((1-(4-(cyanoethynyl)phenyl)-1H-1,2,3-triazol—4-yl)methyl)carbamate (61) : N: : cBu‘I’Z‘ZEE‘I‘nrgaVS'EElS—ée THF waten 25°C 30 minsN\©‘N/\’/\NHBoc To a solution of 43 (1 eq., 51.5 mg, 0.306 mmol) and boc-propargylamine (1 eq., 47.5 mg, 0.306 mmol) in THF (2 mL) were added H20 (1 mL) and on of CuSO4 (10 %, 4.89 mg, 0.0306 mmol) and sodium ascorbate (50 %, 30.3 mg, 0.153 mmol) in water (50 uL each). ng continied for 10 minutes, one more portion of CuSO4 (10 %, 4.89 mg, 0.0306 mmol) and sodium ascorbate (50 %, 30.3 mg, 0.153 mmol) was added.

After another 15 minutes of stirring, EtzO (15 mL) and NH4C1 (sat, 10 mL) were added.

Organic phase was washed two more times with NH4C1 (sat, 10 mL), dried over MgSO4 and evaporated to give 61 (98 mg, 0.303 mmol, 99 %) as a yellow solid. Used without further purification. 1H NMR (400 MHz, CHLOROFORM-d) 67.97 (s, 1H), 7.74 = 8.78 Hz, - 7.81 (m, J 2H), 7.67 = 8.78 Hz, 2H), 4.41 - 7.74 (m, J (d, J = 6.02 Hz, 2H), 1.32 - 1.41 (m, 9H); 13C NMR (101 MHz, CHLOROFORM-d) 6139.0, 135.1, 120.4, 117.8, 107.2, 105.1, 81.3, 64.5, 28.4; ESI-MS: C17H18N502+ [M+H]+, 323.14; found 323.13.

W0 20151001117 79 (1-(4-(cyanoethynyl)phenyl)-1H-1,2,3-triazolyl)methanaminium trifluoroacetate (62): —>*H3N/W/\N < >: 1‘":ka N\©~NMNHBOC DCM 25 °,c 15 hours To a solution of 61 (1 eq., 21.5 mg, 0.0665 mmol) in DCM (1 mL) was added TFA (20 eq., 151 mg, 0.0988 mL, 1.33 mmol). The obtained reaction mixture was left overnight at room temperature (or 2 hours at 37 °C) to the targeted product (22.4 mg, 0.0665 mmol, 100 %) after the evaporation of all volatile compounds. 1H NMR (400 MHz, METHANOL-d4) 88.74 (s, 1H), 7.99 - 8.15 (m, 2H), 7.85 — 7.97 (m, 2H), 4.25 - 4.45 (m, 2H); 13C NMR (101 MHz, METHANOL-d4) 8141.2, 138.9, 135.2, 122.3, 120.3, 117.7, 104.4, 81.1, 62.9, 34.0; ESI-MS: C12H10N5+ [M]+, 227.09; found 227.10.

N-((1-(4-(cyanoethynyl)phenyl)-1H-1,2,3-triazolyl)methyl)(3- (trifluoromethyl)-3H-diazirinyl)benzamide (63): ‘H3N o HATU DIPEA ”MN _, «N DMF, 25 °C. 10 mins ii NzN’ A solution of 4-[3-(trifluoromethyl)-3H-diazirinyl]benzoic acid (1 eq., 57.8 mg, 0.251 mmol), HATU (1 eq., 95.5 mg, 0.251 mmol), and DIPEA (3 eq., 97.4 mg, 0.125 mL, 0.753 mmol) in DMF (2 mL) was added onto 62 (1 eq., 84.7 mg, 0.251 mmol). The obtained on mass was d for 10 minutes and purified by HPLC to give the targeted compound (76.5 mg, 0.176 mmol, 70 %) as a white solid.

ESI-HRMS: F3N7O, 554; found 435.10512.

Compound 63 can be used for a labeling method according to the invention, such as for photolabeling of proteins. wo 2015;001117 80 tert-Butyl (2-((2-(4-(cyanoethynyl)benzamido)ethyl)disulfanyl)ethyl)carbamate (64) : F: K k TEA H N s —> 2 \/\s/ \ANAO ACN,25°C, 10mins CI 0 To a solution of 23 (1 eq., 36 mg, 0.143 mmol) in acn (1 mL) was added a solution of utyl N—{2-[(2-aminoethyl)disulfanyl]ethyl}carbamate (1 eq., 36 mg, 0.143 mmol) and DIPEA (2.12 eq., 39.1 mg, 0.05 mL, 0.303 mmol) in ACN (1 mL). The obtained reaction mixture was left for 10 minutes, then solvents were evaporated and the crude product was purified by flash chromatography to give the targeted product (29.3 mg, 0.0723 mmol, 51 %) as a yellowish solid. 1H NMR (400 MHz, OL-d4) 57.74 = 8.53 Hz, 2H), 7.58 - 7.84 (m, J - 7.74 (m, J: 8.53 Hz, 2H), 3.60 (t, J = 6.78 Hz, 2H), 3.23 - 3.35 (m, 2H), 2.85 (t, J = 6.78 Hz, 2H), 2.71 (t, J: 6.90 Hz, 2H), 1.32 (s, 9H); 13C NMR (101 MHz, METHANOL-d4) 8167.3,157.0,137.3, 133.5, 127.5,120.1, 104.4, 81.5, 78.8, 63.1, 39.3, 39.1, 37.8, 27.4, 26.6; ESI-MS: C19H24N303S2+ [M+H]+, 406.12; found 406.10. (4-(cyanoethynyl)benzamido)ethyl)disulfanyl)ethan-l-aminium trifluoroacetate (65): WO 20151001117 81 HN o TFA F38k —. F DCM, ACN, 0 NH °c, 24 hours B || 3 INI W e4 65 To a solution of 64 (1 eq., 29.3 mg, 0.0723 mmol) in ACN—DCM mixture (1 mL of each solvent) was added TFA (10 eq., 82.4 mg, 0.0537 mL, 0.723 mmol). The obtained reaction mixture was stirred for 24 hours, and evaporated to give the targeted compound 65 (30 mg, 0.0715 mmol, 99 %) as a colorless .

ESI-HRMS: C14H16N3OSZ+, 306.07293; found 306.07312. (4-(cyanoethynyl)benzamido)ethyl)disulfanyl)ethan-l-aminium trifluoroacetate (66): *H3N HO ,0 [co with own, 5,: ~ umPM ,3” || ‘YO || \\N 62 66 62 (0.567 eq., 10.1 mg, 0.0299 mmol) on in MeOH (0.0881 mL) was slowly added to a solution of 2-[4,7,10-tris(carboxymethyl)-1,4,7,l0-tetraazacyclododecanyl]acetic acid (1 eq., 21.4 mg, 0.0528 mmol) in water (0.661 mL). The mixture was cooled by ice and pH was adjusted to 5 using DIPEA (25.2 eq., 172 mg, 0.22 mL, 1.33 mmol). An aqueous solution of EDC (0.65 eq., 6.59 mg, 0.0344 mmol) was added dropwise and stirred for 20 min with ice cooling. pH was raised to 8 using DIPEA and reacted for 30 min at room temperature. The end point of the reaction was monitored using HPLC.

WO 01117 82 ESI-HRMS: C28H35N907+, 609.26594; found 609.26417.

Compound 66 can be used as a chelating agent.

WO 2015001117 83 -((4-((4-(2-Cyano((2-(4-((4-((E)-(2,5-dimeth0xy((E)-(4-nitr0phe- nyl)diazenyl)phenyl)diazenylphenyl)- (methyl)amino)butanamid0)ethyl)thi0)vinyl)phenyl)amin0) oxobutyl)carbam0yl)(6-(dimethylamino)(dimethyliminio)-3H-Xanthen yl)benzoate (A): N\‘N o A I cystamine ride I HC| AcONa O O N\\N | —’ N2+CI Hzoacetone (11) N\\N TEA, HBTU, DMF/DOM 052,102 Fast BlackK © OH BHQ-Z-SH NH2 —> HBTU, TEA, DMF DIPEA, ACN WO 2015001117 84 4-((4-((E)-(2,S-Dimethoxy((E)-(4-nitrophenyl)diazenyl)phenyl)diazenyl)phenyl)( methyl)amino)-butanoic acid (BHQ-2).

Fast Black K hemi (zinc chloride) salt (practical grade, z30% dye content) (7.76 g) was suspended in cold water (150.0 mL, 0°C) and stirred for 20 minutes. The suspension was d, and the red solution was added dropwise to a cold (0 oC) mixture of 4- (methyl(pheny1)amino)butanoic acid (1.33 g, 6.88 mmol), concentrated hydrochloric acid (3.1 mL) and sodium acetate (3.6 g, 43.90 mmol) in water-acetone mixture (1:1) (150.0 mL). The reaction mixture was d at 10 °C for 15 minutes and at room temperature for 2 hours. Then the on crude was extracted with ethyl acetate (3x150 mL) and the combined organic layers were dried over Na2SO4. The crude product was purified by column chromatography on silica gel (100% EtOAc, then 100% DCM to DCM/MeOH (95:5)). BHQ-2 (1.36 g, 39%) was obtained as a dark Violet solid. 1H NMR (400 MHz, METHANOL-d4) 5 8.31 (d, J = 9.0 Hz, 2H), 8.00 (d, J = 9.0 Hz, 2H), 7.86 (d, J = 9.0 Hz, 2H), 7.45 (s, 1H), 7.40 (s, 1H), 6.77 (d, J = 9.0 Hz, 2H), 4.05 (s, 3H), 4.00 (s, 3H), 3.5 (t, J: 7.1 Hz, 2H), 2.36 (t, J: 7.1 Hz, 2H), 1.98-1.90 (m, 2H); 13C NMR (101 MHz, METHANOL-d4) 5 176.2, 157.1, 154.3, 153.0, 151.4, 149.0, 147.4, 145.0, 142.6, 126.9, 125.3, 124.2, 112.1, 101.7, 100.7, 57.2, 52.3, 39.0, 31.6, 22.9. 65b: 4-((4-((E)-(2,5-Dimethoxy((E)-(4-nitrophenyl)diazenyl)phenyl)diazenyl)phe nyl)(methyl)amino)-N-(2-mercaptoethyl)butanamide ((BHQ-2)-SH).

BHQ-2 (1 eq., 92.2 mg, 0.182 mmol) was dissolved in a mixture of DMF (5 mL) and DCM (10 mL). TEA (6 eq., 152 uL, 1.09 mmol) and cystamine dichloride (5 eq., 204 mg, 0.91 mmol) were added. The mixture was cooled to 0 °C and HBTU (1 eq., 69 mg, 0.182 mmol) was added. The solution was allowed to reach room ature and stirred for 15 hours. When total sion was d, DTT (6 eq., 168 mg, 0.162 mL, 1.09 mmol) was added. After the resulting mixture has been stirred for 10 minutes at room temperature, the crude was diluted with saturated NaHCOs solution (75 mL) and extracted with EtOAc (2x50 mL). The organic layers were combined, washed with water (50 mL), brine (50 mL) and dried over Na2SO4. The crude product was d by column chromatography on silica gel (DCM/MeOH from 100:0 to 95:5) to yield (BHQ-2)-SH (60.7 mg, 0.107 mmol, 59 %) as a dark Violet solid.

W0 20151001117 85 2014/064387 1H NMR (400 MHz, CHLOROFORM-d) 5 8.33 (d, J = 9.0 Hz, 2H), 8.0 (d, J = 9.1 Hz, 2H), 7.9 (d, J = 9.1 Hz, 2H), 7.42 (s, 1H), 7.42 (s, 1H), 6.75 (d, J = 9.00 Hz, 2H), 5.90 (t, J: 5.6 Hz, 1H), 4.06 (s, 3H), 4.01 (s, 3H), 3.49 (t, J: 7.4 Hz, 2H), 3.41 (dt, J: 6.2, 6.4 Hz, 2H), 2.64 (td, J = 6.4, 8.47 Hz, 2H), 2.24 (t, J: 7.4 Hz, 2H), 2.01-1.94 (m, 2H); 13C NMR (101 MHz, CHLOROFORM-d) 6 172.2, 156.6, 153.8, 152.4, 151.1, 148.5, 147.0, 144.7, 142.3, 126.4, 124.9, 123.7, 111.6, 101.2, 100.3, 57.0, 56.9, 51.8, 42.5, 38.7, 33.4, 24.9, 23.0; HR—ESI-MS: C27H31N705S, 565.2107; found 05. 67: 5-((4-((4-(Cyanoethynyl)phenyl)amino)oxobutyl)carbamoyl)(6-(dimethyla mino)(dimethyliminio)-3H-Xanthenyl)benzoate.

To a cooled to 0 °C degased solution of 62a (1 eq., 17.3 mg, 0.0507 mmol) and TAMRA-5’—COOH (1 eq., 21.8 mg, 0.0507 mmol) in DMF (1.4 mL), HBTU (1 eq., 19.2 mg) was added at 0 °C. Obtained reaction mass was stirred for 5 minutes and TEA was added. The reaction mass was stirred for 1 hour at 25 OC, ated and purified by HPLC to yield 65a (22 mg, 68%) as a dark—violet solid. 1H NMR (400 MHz, METHANOL-d4) 8 8.8 (br. s, 1H), 8.7 (s, 1H), 8.08 = - 8.16 (d, J 8.2 Hz, 1H), 7.60 = 8.9 Hz, 2H), 7.49 = 8.9 Hz, 2H), 7.32—7.39 - 7.70 (d, J - 7.58 (d, J (d, J: 8.2, 1H), 8 7.01 (s, 4H), 6.93 (s, 2H), 3.48-3.58 (m, 2H), 3.26 (s, 12H), 2.44-2.54 (t, J = 7.17 Hz, 2H), 1.98-2.12 (m, 2H); 13C NMR (101 MHz, METHANOL-d4) — not informative; HR—ESI-MS: 639.24817; found 639.24310.

A: 5-((4-((4-(2-Cyano-l-((2-(4-((4-((E)-(2,5-dimethoxy((E)-(4-nitrophenyl )diazenyl)phenyl)diazenylphenyl)- (methyl)amino)butanamido)ethyl)thio)vinyl)phenyl)amino) oxobutyl)carbamoyl)(6-(dimethylamino)(dimethyliminio)-3H-Xanthen yl)benzoate.

To a degased solution of BHQ-SH (1.13 eq., 2 mg, 0.00354 mmol) in DCM (0.5 mL), a d solution of 67 (1 eq., 2 mg, 0.00313 mmol) in methanol (0.5 mL) was added.

TEA (4.6 eq., 2 uL, 0.0144 mmol) was added and the obtained reaction mass was left overnight at 25 oC. Solvents were evaporated; the crude product was solubilised in DMSO (0.5 mL) and purified by HPLC to give BHQ-APN—TAMRA (A, 2.7 mg, 0.00225 mmol, 72%) as dark—Violet solid. 1H NMR (400 MHz, METHANOL-d4) 8 8.63 (d, J = 2.0 Hz, 1H), 8.34 (d, J = 8.8 Hz, 2H), 8.22 (dd, J = 7.8, 2.0 Hz, 1H), 8.00 (d, J = 8.8 Hz, 2H), 7.75 (d, J = 9.0 Hz, 2H), WO 2015001117 86 7.69 (d, J = 8.5 Hz, 2H), 7.53 (d, J = 8.0 Hz, 1H), 7.39 (d, J = 8.5 Hz, 2H), 7.34 (d, J = 9.0 Hz, 2H), 6.75-6.86 (m, 8H), 5.48 (s, 1H), 4.02 (s, 3H), 3.92 (s, 3H), 3.58-3.63 (m, 2H), 3.45—3.52 (m, 2H), 3.21 (s, 12H), 3.16 (t, J = 6.9 Hz, 2H), 3.08 (s, 3H), 2.71 (t, J = 6.5 HZ, 2H), 2.55 (t, f = 6.2 HZ, 2H), 2.22 (t, J = 6.9 HZ, 2H), 2.08—2.16 (m, 2H), 1.88- 1.96 (m, 2H), 1.61 (br.s, 1H); 13C NMR (101 MHz, METHANOL-d4) — not informative; HR-ESI-MS: C65H65N1201OSJr , 120546618; found 120546748. -((3-(3-((2-(4-((4-((E)-(2,5-Dimethoxy((E)-(4-nitrophenyl)diazenyl)phenyl)diaze nyl)phenyl)(me- thyl)amino)butanamido)ethyl)thio)-2,5-dioxopyrrolidinyl)propyl)carbamoyl)( 6-(di-methylamino)—3—(dimethyliminio)-3H-Xanthenyl)benzoate (B): E G 1. A toluene A Br/\/\NHBOC O , O O O 2. TFA, DCM N N 5—TAMRA TFA- —. —. —> K2003, DMF HBTU, TEA, DMF O O +HBN BocHN B-4 B-3 B-2 (BHQ—2)—SH (65b), DCMzMeOH B-4: 3a,4,7,7a-Tetrahydro-1H-4,7-epoxyisoindole-1,3(2H)-dione.

This compound was sised according to the previously described procedure. 845 W0 20151001117 87 2014/064387 B-3: tert-Butyl (3-((3aR,7aS)-1,3-dioxo-33,4,7,7a-tetrahydro-1H- 4,7-epoxyisoindol-2(3H)-yl)propyl)carbamate.

To the solution of B-4 (1 eq., 1.76 g, 10.7 mmol) and tert—butyl N—(3- ropyl)carbamate (2 eq., 5.07 g, 21.3 mmol) in DMF (20 mL), K2COs (1.2 eq., 1.77 g, 12.8 mmol) was added. The obtained reaction mass was heated at 50 °C for 18 hours. The solution was left to cool down; a solid e was filtered and washed with DMF. United organic fractions were evaporated, hexane (50 mL) was added to the obtained slurry mass. Obtained suspensions were stirred for another hour, filtered and washed with hexane to give B-3 (3.36 g, 10.4 mmol, 98 %) as white solid. 1H NMR (400 MHz, CHLOROFORM-d) 8 6.49 (s, 2H), 5.23 (s, 2H), 3.52 (t, J = 6.5 Hz, 2H), 2.96 — 3.09 (m, 2H), 2.82 (s, 2H), 1.66-1.75 (m, 2H), 1.41 (s, 9H); 13C NMR (101 MHz, CHLOROFORM—d) 8 176.5, 155.9, 136.5, 81.0, 79.3, 47.5, 37.1, 36.0, 28.4, 27.8.

B-2: 1-(3-Aminopropyl)-1H-pyrrole-2,5-dione (TFA salt).

A solution of 66c (1 eq., 243 mg, 0.754 mmol) in toluene (25 mL) was d for 3 hours. Toluene was evaporated; the obtained white crude product was resolubilised in DCM (5 mL), TFA (0.5 mL) was added. Stirring was continued for 2 hours until complete disappearance of a ng material (controlled by TLC). t were evaporated after the reaction was ed by methanol (3 mL). Obtained l-(3- aminopropyl)—1H-pyrrole-2,5-dione (B-2, TFA salt, 190 mg, 94%) was used without fiarther purification. 1H NMR (400 MHz, METHANOL-d4) 5 6.76 (s, 2H), 3.52 (t, J = 6.7 Hz, 2H), 2.80- 2.88 (m, 2H), 1.76-1.88 (m, 2H); 13C NMR (101 MHz, METHANOL-d4) 8 170.6, 135.6, 38.5, 35.4, 28.0.

B-l: 2-(6-(Dimethylamino)(dimethyliminio)-3H-xanthenyl)((3-(2,5-dioxo-2, S-dihydro-IH-pyrrolyl)propyl)carbamoyl)benzoate (TAMRA-maleimide): To a solution of TAMRA-5’-COOH (1 eq., 71.5 mg, 0.166 mmol) in DMF (3.21 mL), TEA (2.5 eq., 57.7 uL, 0.415 mmol) and HATU (1.12 eq., 70.7 mg, 0.186 mmol) here added. Obtained reaction mass was stirred for another 5 minutes and B-2 (1 eq., 71.5 mg, 0.166 mmol) was added. Stirring continued for 25 minutes and the reaction mass was evaporated under reduced pressure to the volume of about 1 mL, and the reaction WO 2015001117 88 mass was purified by preparative HPLC to give TAMRA-Maleimide (B-l, 34.8 mg, 0.0615 mmol, 37 %) as a pink solid. 1H NMR (400 MHz, METHANOL-d4) 5 8.66 (d, J: 1.8 Hz, 1H), 8.14 (dd, J: 1.8, 8.0 Hz, 2H), 7.41 (d, J = 8.0 Hz, 2H), 7.02 (d, J = 9.5 Hz, 1H), 6.92 (dd, J = 9.5, 2.2 Hz, 2H), 6.81 (d, J = 2.2 Hz, 2H), 6.72 (s, 2H), 3.52 (t, J: 6.8 Hz, 2H), 3.34 (t, J: 7.0 Hz, 2H), 3.17 (s, 12H), 1.80-1.90 (m, 2H); 13C NMR (101 MHz, METHANOL-d4) 8 172.5, 168.2, 167.4, 160.6, 159.0, 158.9, 138.1, 137.7, 137.6, 135.5, 132.9, 132.3, 132.0, 131.4, 115.6, 114.8, 97.5, 82.4, 41.0, 38.6, 36.4, 29.3. HR-ESI-MS: C32H30N406, 653; found 566.21654.

B: 5-((3-(3-((2-(4-((4-((E)-(2,5-Dimethoxy((E)-(4-nitro- phenyl)diazenyl)phenyl)diazenyl)phenyl)(methyl)amino)bu- tanamido)ethyl)thio)-2,5-dioxopyrrolidinyl)propyl)car— bamoyl)(6-(dimethylamino)(dimethyliminio)-3H-Xanthenyl)benzoate.

To a degased solution of BHQ—SH (1.15 eq., 4.6 mg, 0.00812 mmol) in DCM (0.5 mL), a degased solution of Maleimide (B-1) (1 eq., 4 mg, 0.00313 mmol) in methanol (0.5 mL) was added. TEA (5 eq., 5 uL, 0.0353 mmol) was added and the obtained on mass was left overnight at 25 oC. Solvents were evaporated; the crude product was solubilized in DMSO (0.5 mL) and purified by HPLC to give B (7 mg, 0.00621 mmol, 88%) as dark-violet solid. 1H NMR (400 MHz, DMSO-d6) 8 8.91 (t, J: 6.1 Hz, 1H), 8.68 (s, 1H), 8.43 (d, J: 9.1 Hz, 2H), 8.31 (d, J: 8.9 Hz, 1H), .10 (m, 3H), 7.77 (d, J: 9.1 Hz, 2H), 7.60 (d, J = 7.8 Hz, 1H), 7.39 (s, 1H), 7.33 (s, 1H), 6.99 (s, 3H), 6.89 (s, 1H), 6.85 (d, J: 9.1 Hz, 2H), 4.04 (dd, J = 3.9, 8.9 Hz, 1H), 3.98 (s, 3H), 3.92 (s, 3H), 3.41—3.45 (m, 2H), 3.27- 3.38 (m, 6H), 3.23 (m, 12H), 3.06 (s, 3H), 2.85-2.95 (m, 1H), 2.72-2.81 (m, 1H), 2.52- 2.56 (m, 2H), 2.17 (t, J= 7.3 Hz, 2H), 1.74-1.88 (m, 4H). HR-ESI-MS: C59H62N11O11S+ [M+H]+, 1132.43455; found 1132.43384.

Example 2: Labeling of a cysteine derivative with compounds of the invention WO 20151001117 89 :N + —.

ACHN R|:/\)LNHBnNHAc R4 NHBn 1-12 AcCysNHBn General procedure To a vial ning 985 11L of PBS (1x, pH 7.6), were subsequently added 5 11L of the stock solution of benzamide (10 mM in water), 5 nL of the stock solution of arylpropiolonitrile (1-12, 10 mM in DMSO) and 5 ML of stock on of AcCysNHBn (7m, 10 mM in DMSO). Aliquots of the reaction mixture (50 1.1L) were ed by HPLC (injection at 0 and 30 s of reaction). Areas under the peaks of the starting materials and hydrolysis products were normalized according to the area of the peak of the internal standard.

Results Obtained results are summed up in table 2 below, which presents the conversion of the compounds 1-12 in 30 s in presence of 7m at 50 11M concentration of each reagent and 25°C. The reaction is extremely sensitive to steric hindrances induced by substituents in ortho-position to propiolonitrile group (entries 1, 5, 8-9, 4) as well as to onic effect of the substituent: -I and -M substituents increase (entries 10 and 12), while +M substituents decrease the reactivity of the compound (entries 3 and 7). .1% 70.4% * 46.8% .-CONHMe 85.5% -I_———E- * Byproducts ** conversion in 60 minutes. were observed; Table 2 Exam le 3: H drol ‘c stabilit of a com ound of formula I and com arison with phenylmaleimide WO 20151001117 90 To a vial containing 980 uL of PBS (1X, pH 7.6), were subsequently added 10 uL of a stock solution of benzamide and 10 uL of a stock solution of electrophile ACN : :N (phenylmaleimide 1 or 11) to give final concentration of 1 mM (both internal rd and electrophile). Aliquots of the on mixture (50 uL) were analyzed by HPLC for 5 hours of hydrolysis (injection every 30 min). Areas under the peaks of the starting materials and hydrolysis products were normalized according to the area of the peak of the internal standard.

The obtained results are ted in figures 4 and 5. Noticeable hydrolysis was observed only for phenylmaleimide 1 (PhMal, kobs = 7x10‘ss'1). llshowed no able change in concentration.

Example 4: Stability of compounds of formula 11111 > Stabilit ofthe followin com ound in different conditions A 100 mM stock on of the “addition product” NHBn was prepared in DMSO and stored at -20°C. 1 uL of the stock solution was added to 999 uL of working solutions to give 100 uM final concentration of substrate. Aliquots were analyzed at 0, and 60 min. Areas under peak of starting material were normalized according to the area of the peak of the internal standard mide). All ements were carried at °C.

Table 3 below shows the conversion of “the addition product” in different media in one hour.

WO 20151001117 91 # Working solution Conversion of “addition product” in lh 100 mM PhSH in PBS(7.4):DMSO=80:20 Table 3 This experiment clearly show that the addition t is stable and undergoes very little degradation in a wide range of conditions, in particular for pH ranging from 0 to In addition, hardly any thiol exchange is observed when the addition product is exposed for 1 hour to a medium comprising an excess of another thiol, such as phenylthiol or glutathione. > Stabilit of a com ound of formula III and com arison with ide The stability of compounds A (according to the ion) and B ence compound) below was studied in different biological conditions.

Cell culture: WO 20151001117 92 Normal liver BNL CL.2 cells from mouse were grown in Dulbecco’s MEM medium with lg/l glucose (Eurobio, Les Ulis, France) mented with 10% fetal bovine serum (Perbio, Brebieres, ), 2 mM amine, 100 U/mL penicillin, 100 ug/mL streptomycin (Eurobio). Cells were maintained in a 5% C02 humidified atmosphere at 37°C.

Microscagy .' Twenty four hours prior to experiment, 2.5x104 BNL CL.2 cells were seeded per well in 8-well Lab-Tek II Chambered coverglass plates (ref , Nunc, Naperville, IL, USA). The required amounts of probes A and B were diluted up to 300 pl in MEM complete medium to give final concentration of 1 uM and then added onto the cells. A 5 ug/ml of Hoechst ll8 solution was used as a nuclear . Cells were observed with a confocal Leica TSC SPE II microscope after washing with 10% FBS red phenol free Eagle’s MEM medium.

Cytometfl: The day before experiment, BNL CL.2 cells were seeded in 96-plates (Greiner Bio One, Frickenhausen, Germany) at 2.0x104 cells/well in Dulbecco’s MEM complete medium.

Both probes (A and B) were prepared at 1 uM concentrations in Dulbecco’s MEM complete and added onto cells during ent times (2, 6 and 24 hours). After washing with PBS (Eurobio), 5 min incubation with 40 ul ne, and addition of 160 ul of PBS EDTA 5 mM, cells were analyzed by flow cytometry on a PCA-96 Guava cytometer (Guava Technologies Merck Millipore, Billerica, MA, USA) with a green laser.

First, compound A was far more stable than compound B in human plasma (see fig 1). , compound A was far more stable than compound B in celluto (see fig 2).

Example 4: Selectivity of compounds of the invention towards the thiol moiety Screening for selectivity was done on benzylamides of non-protected amino acids. 100 mM stock solutions of benzylamides of amino acids (in form of TFA salts) and electrophiles (phenylpropiolonitrile and phenylmaleimide) were prepared in DMSO and stored at -20°C. A 100 mM stock solution of benzamide (used as an internal standard) was prepared in led water and stocked at -20°C. Analyses of reaction mixtures W0 20151001117 93 were ted with Shimadzu LC with SunFireTM C18 5 uM 4.6x150 mm column (Waters). HPLC parameters were as follows: flow rate 1 mL/min, gradient from 5 to 95% of mobile phase B from 0 to 20 min, followed by 5 min at 95% of mobile phase and post time of 5 min. Mobile phase A was 0.05% TFA in water (mQ) (V/V), and mobile phase B was acetonitrile (HPLC grade). Data were analyzed using Shimadzu analysis re. Signals were normalized according to the area of the peak of the internal standard (benzamide). Areas under the peaks of the amino acid benzylamides were used to calculate their conversion during on. uL of the stock solution of amino acid benzamide and 2.5 uL of the stock solution of benzamide were added to a vial containing 977.5 uL of PBS (lx, pH 7.6). The solution was stirred and 10 uL of the stock solution of electrophile were added to give 1 mM final concentrations of reagents and 0.25 mM concentration of benzamide. Aliquots of the reaction mixture (50 uL) were analyzed by HPLC for 1 hour of hydrolysis (injections at 0, 30 and 60 min). Areas under the peaks of the ng materials and hydrolysis products were normalized according to the area of peak of the internal standard. In case of phenylpropiolonitrile, none of amino acid models gave more than 1.6% conversion (see table 3 below). Conversely, when phenylmaleimide was tested, some amino acid benzylamides showed sions up to 8.5%. Masses of corresponding adducts were detected by mass spectrometry (ESI-LCMS) in some cases (shown in bold, Table 4).

Table 4 below ts the conversion of benzylamides in 1 hour in PBS (1X, pH 7.6) in presence of phenylpropiolonitrile (l).

Amino acid ide ‘WmmmmmcfliiiéigimdnwMMMMMMMMMM Amino acid benzamideml Conversion Bn {7a) 98% TerHBn (754‘) l 1.5% GlyNHBn. {7b} 0.39»; HisNHBn {711} 1 0.15% n (‘70) [IL 1% GluNHBu {7? 0.1% ValNHBn (7.11 0.7% ”frpNHBu £15“? 1.3% SerNHBn (7e) 03% AJ'ENHBH (7k) 0.4% L MetNHBn or; J 0.1% J A§pNHBfl {'70 I 0.0020 Table 4 Table 5 below presents the conversion of benzylamides in 1 hour in PBS (1X, pH 7.6) in presence of phenylmaleimide. Bold values correspond to those for which the mass of the corresponding adduct was detected by ESI-LCMS.

WO 20151001117 94 Amino acid benzamida sion ! Amino acid ide [ Conversion zsNHBu {7a} 100 i 1* W331: r7 GWN‘EEIBI: (7b) ‘ HisN‘HBn (firm AlaNHBn {702 0.290" (WHNH {7%) W ‘ VaINHBn (7d) 0. 9% . TIpNHBu £31} 1.0% SerNHBn [7a) 2.8% if 7k) 2 .99»; 4 ArgNHBn MetNHBn (71') 1.9% AspNHBn (‘71) l. 3% Table 5 In conclusion, the selectivity of compounds of the invention towards the thiol moiety when compared to other moieties is clearly higher than the selectivity obtained for corresponding compounds, wherein the propiolonitrile moiety is replaced with a maleimide moiety.

Example 5: ty tests Toxicity of the following “linker” compounds of formula (II) was studied by MTT assay on HaCaT cell lines: N N N N N N N N || || || II II || || || II II || || || || || || OMe NH2 N02 OMe NH2 NHAC 2 3 5 7 11 1O In Vitro xicity was measured using an MTT (3-(4,5-Dimethylthiazolyl)- 2,5-diphenyltetrazolium bromide) assay. The experiments were performed in 96—well plates with HaCaT cells grown to confluence in cell culture media (RPMI 1640 media mented with 10% fetal calf serum and 1 mM Glutamin, 200 uL per well). Cells were incubated with chemical reagent at different concentrations (100 uM to 0.78 uM by serial 1/2 dilutions) at 37°C for 24 hours. After incubation, the supernatant was replaced with fresh culture media ning MTT (300 ug/mL). After 2 hours of incubation at 37°C, the media was carefully removed and 100 uL ofDMSO were added WO 20151001117 95 to dissolve the formazan crystals generated by mitochondrial enzymes-induced reduction of the MTT. The absorbance was measured at 595 nm using a microplate reader (Biotek, Synergy HT). The cell viabilities were expressed as percent of ted control cells.

The results of the MTT test are presented on figure 5, and clearly show that nds of formula (II) are not toxic and may thus be used for ce for biological applications.

Example 6: Labeling of lysozyme with a compound of formula (11: Labeling of tryptic digest of lysozyme 1 nmol of lysozyme was solubilized in NH4HC03 (25 mM) and d with lmM of TCEP at 57°C during 1 hour. A solution of APN—TMPP (lmM in DMSO) was added to the protein at a molar ratio of 1:200. Then, labeled protein was subjected to proteolysis by porcine trypsin (Promega V5111). Sample was digested with 1:100 (w/w) trypsin in mM ammonium bicarbonate at 35 °C overnight. NanoLC-MS/MS analyses were performed to follow the reaction. The ing peptide mixtures were analyzed by C18 reversed phase nanoHPLC on a nanoACQUITY Ultra-Performance-LC system (Waters, Milford, MA) coupled to a Q-TOF maXis (Bruker ics, Bremen, Germany) mass ometer equipped with a nano—electrospray source. Chromatographic separation was performed on a nanoACQUITY Ultra-Performance-LC. The peptides were separated on an ACQUITY UPLC® BEH130 C18 column (Waters Corp), 75 um x 200 mm, 1.7 um particle size. The solvent system ted of 0.1% formic acid in water (solvent A) and 0.1% formic acid in acetonitrile (solvent B). Trapping was performed on a 20 x 0.18 mm, 5 um ry C18 pre-column (Waters Corp.) during 3 minutes at 5 uL/min with 99% of solvent A and 1% of solvent B. Elution was performed at a flow rate of 300 nL/min, using a 1-50% gradient of t B for 30 minutes at 50°C followed by a fast rise at 80% (5 minutes) of solvent B. The complete system was fully controlled by Hystar 3.2 (Bruker Daltonics). The Q—TOF ment was operated with the ing settings: source temperature was set to 200°C, drying gaz flow was 4 l/h, and the nano-electrospray voltage was 4kV. Mass calibration of the TOP was achieved WO 20151001117 96 using ES-TOF Tuning Mix (Agilent Technologies) on the 50 to 2200 m/z range in positive mode. For tandem MS ments, the system was operated with automatic ing between MS and MS/MS modes both on m/z range [50-2200]. In MS the summation time was 0.2 s. In MS/MS summation time was weighted between 0.2 s and 1.4 s in fiinction of parent ion ity. The 2 most abundant es (intensity threshold 400 au), preferably ions with two, three, four or five charges, were selected on each MS spectrum for further isolation and CID fragmentation with 2 es set using collision energy profile. Fragmentation was med using argon as the collision gas.

Tryptic peptides were manually sequenced (de novo) to confirm their sequence and locate the cysteine tagged by the AFN-TMPP probe. The peptides were identified using extracted ion chromatograms (EIC) based on monoisotopic mass of calculated peptide sequences.

Evaluation of APN—TMPP chemoselectivity was carried by studying of its reaction with tryptic digest at 200:1 molar ratio of APN-TMPP (luM) to protein (around 10:1 to cysteine moieties) at room temperature for one hour. Peptide mixtures obtained without and with chemical tization were analyzed by LC-MS/MS. All detectable cysteine- containing es reacted with a probe and were delayed while cysteine-free peptides were unaffected. The labeling efficiency was evaluated based on the ratio between ities of labeled and non-labeled peptides by LC-MS. More than 98% of the detected peptides were completely labeled. LC-MS results show y that cysteine- containing peptides have an increased retention time due to the on of the hydrophobic TMPP group, whereas the retention time of all other peptides was unchanged (Table 6).

Table 6 below shows the results of LC-MS analyses of tryptic digest of lysozyme before and after reaction with APN—TMPP.

WO 20151001117 97 Elem“: tagging After tagging Pepwe cem r1112 (charge state} RT 1min} mix (charge stale) RT {min} ARR-11m} Number 91 tags “cswmmx” mam (+2) 13.9 545189 (+3.1 21.2 111.3 1 ”CELWMQXKZ" 426w 1+2) 116 551123 1+3} 2a? 1171 1 vacAAK” 634131 (+2) 19.8 889.96H11) 2&3 as 1 Memo?" assess 1+2) 16.5 516122113} 25.? 9‘2 1 ”Niculpcsmtssmmsmcm’“ 1mm {12; 23.7 919211 (+5} 30.3 as :1 ”Fasxmmnmn“ m“ 1331412} 1:15 1’1483 1+3) 137.5 a 0 ‘Werovmwmm 523127 1+2} am 52:12? 1+2) 1?.3 a a "N'Toesrommmssm 555123 1+2; 1331 535.23 (+2} 13.2 a 11 “*wsoommmwmwam 553.27 112) a u 559,27 1+2) ‘ 31149 ‘‘‘‘‘ “Maura V m {a} Cysteine residues are in hold“ Table 6 Example 7: Conjugation of solubilizating APN ts (49-54) with CD38 A275C mutant.

General scheme of the experiment (on the example of modification of CD38 mutant with 49) is illustrated on Figure 6.

To 300 ML of CD38C275 solution (1 mg/mL) was added 6 ML of 50 mM on of solubilizing APN reagent (49-54) in DMSO. In parallel, as a control, to 300 uL of CD38C275 was added 6 1.1L of DMSO. Both samples were incubated for 15 hours at 25 °C, then dialyzed 5 times (membrane cut off of 10k) to give final volume of 30 11L each (10 mg/mL). Size of ates was measured by DLS.

Exam le 8: Labelin of CD38-CD375 mutant and com arison with maleimide a) Stabilit of the com ound of the invention and of the corres ondin maleimide The compounds below were synthesized:.

WO 20151001117 98 Stability s proved that the compound according to the invention was stable for 24 hours in PBS (Phosphate Buffer Saline). Comparatively, the corresponding compound comprising a ide moiety was 70% degraded after one hour in PBS. b) Reaction with the CD38 mutant Both compounds were reacted with a 2 uM solution of the CD3 8-C375 mutant.

Gel electrophoresis after purification showed that a higher labeling rate could be ed with the compounds according to the invention than with the corresponding maleimide compound. Figure 7 ts the gel electrophoresis ed with the compound of the invention and the maleimide, before and after purification.

Example 9: Conjugation of Trastuzumab and TAMRA using compound 18 General scheme of the experiment is illustrated on Figure 8.

To the solution of Trastuzumab (lOOuL, 10 mg/mL in 50mM borate buffer pH 8.5) was added 1.74 uL of the on of 18 (10 mg/mL in DMSO). After incubation for 1h at °C was added 0.69 uL of TAMRA-SH (lOOmM in DMSO). The mixture was incubated at 25°C for 16h and the conjugate was purified by size exclusion chromatography.

The comparison experiment was carried out using 4-(N— maleimidomethyl)cyclohexanecarboxylic acid N—hydroxysuccinimide ester (SMCC) d of 18.

SDS-PAGE analysis of the obtained conjugates (Figure 9) showed that compound 18 allows for higher levels of conjugation comparing to SMCC.

Native ESI-MS analysis of the conjugate prepared using 18 (Figure 10, Figure 11) showed that in average one le ofTAMRA per antibody was conjugated.

Native ESI-MS analysis of the conjugate prepared using SMCC (Figure 12, Figure 13) showed a complex mixture ofundistinguishable species.

Experiment shows that the compound 18 allows for higher levels of conjugation and gives cleaner population of conjugates comparing to generally applied SMCC.

WO 2015001117 99 2014/064387 Example 10: Direct conjugation of the compound 58 to partially reduced Trastuzumab.

General scheme of the experiment is illustrated on Figure 14.

To the solution of Trastuzumab , 10 mg/mL in 50mM PBS pH 7.4 with 10mM of EDTA) was added the on of TCEP (10 mM in water, 1.1 or 2.2 eq.). The mixture was incubated at 37°C for 2h and then the solution of 58 (8.25 ML, 10 mM in DMSO) was added. The mixture was incubated at 25°C for 16h and the conjugate was purified by size exclusion chromatography.

SDS-PAGE analysis of the obtained conjugates (Figure 15) showed that compound 58 was covalently attached to the antibody. ESI-MS analysis showed that in e 4 molecules were conjugated per antibody using 2.2 eq. of TCEP.

Example 11: ging of antibody fragments using compounds 33 and 34.

General scheme of the experiment is illustrated on Figure 16.

To the solution of zumab (lOOuL, 10 mg/mL in 50mM PBS pH 7.4 with 10mM of EDTA) was added the solution of TCEP (10 mM in water, 5 eq.). The mixture was incubated at 37°C for 2h and then the solution of 33 or 34 (10 mM in DMSO, 15 eq.) was added. The resulting solution was incubated for 16 h at 25°C and then analyzed by SDS-PAGE in reducing conditions.

SDS-PAGE analysis showed that antibody fragments were successfully bridged by compounds 33 and 34 (Figure 17).

Claims (4)

1. Process for bioconjugation of a protein comprising at least one cysteine e having a thiol moiety with an antibody, a drug or a fluorescent probe, comprising 5 contacting a protein comprising at least one cysteine residue having a thiol moiety with a compound of formula (I): (I) , wherein each of R1 to R5 is independently selected in the group consisting of: - hydrogen atoms, 10 - alkyl, alkene or alkyne groups, optionally upted by at least one heteroatom selected among O, N and S, - aryl groups, - alkoxy groups, - n atoms, 15 - -NRR’ groups, - -ONH2 group, - -NH-NH2 group, - -NO2 group, - -N3 group, 20 - -N2+ group, - maleimide group, - -C(=O)OR groups, - -C(=O)R groups, - -OH group, 25 - -B(OR’’)2 group, - phosphine or phosphonium groups, - -N=C=O or -N=C=S group, - -SO2Cl group, - a -O-C(=O)-C(N2)-CF3 group or a -C(=O)-C(N2)-CF3 group, 30 - activated esters, such as -NHS, perfluorinated esters and acylureas, - a -C≡C-C≡N group, and - alkyl groups substituted by at least one of the previously listed groups, wherein R and R’ are ndently hydrogen atoms, alkyl, alkene, alkyne or aryl groups and R’’ is a hydrogen atom or an alkyl group, and 5 wherein at least one of R1 to R5 comprises a tag moiety which is optionally bonded to the phenyl ring h a linker group and which is selected from an antibody; a drug; or a fluorescent probe.

2. A compound of the formula (I): 10 (I) , wherein R1 to R5 are as defined in claim 1, provided that the compound is not [3-(3-formyl-phenylethynyl)-phenyl]-propyne nitrile

3. A compound selected from the group consisting of: 103 103 \ / o ”N O INI INI 26 27 l \ N | \ N |+ \ —FL+— \ l ‘ N\ Hm) _N+_ N H 0 o /\ 0 O 0 F F 0 / GAO F F / F F \ I / FmocHN F F \ I F F SO3Na \ F F F O OH 32 SO3Na 33 36 N N H H _N/ N C L £1 \9 O O O 18F CF218F 125' L \\ 37 38 39 43 44 \\N HN O 9 . 5

4. A compound of formula (III): (III) , n R1 to R5 are as described in claim 1, and wherein R6-SH is a protein comprising at least one cysteine residue having a thiol moiety. W0 20151001117