5.3 Synthesis
5.3.1 General synthetic procedures
The following standard procedures A-Q for the synthesis of precursors, intermediates, and inhibitors were performed as described previously in several textbooks.97, 98
Method A
Loading of Fmoc amino acids on 2-Cl-tritylchlorid (2Cl-Trt-Cl) resin
The Fmoc amino acid (1 equiv) was suspended in dry DCM and treated with 4 equiv DIPEA to reveal a clear solution, which was added to 1 equiv resin in a polypropylene-syringe for manual SPPS equipped with a PTFE filter (Intavis Bioanalytical Instruments, Köln). After 2 h shaking at RT, the reaction solution was removed, and the resin was washed 3 1 min with DCM/MeOH/DIPEA (17:2:1, v/v/v), followed by
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multiple washing with DCM, DMF and again with DCM. The loaded resin was dried in vacuum.
Method B
Loading of diamines on tritylchlorid resin
The amino component (4 equiv) was dissolved in dry DCM and loaded to the tritylchloride resin as described on method A, followed by an identical washing procedure. If the amines were used as salts additional 4 equiv DIEPA was added.
Method C
Fmoc solid phase peptide synthesis
The manual Fmoc SPPS was performed in 2 or 5 mL polypropylene-syringes (Multisynthech GmbH, Witten, Germany) equipped with PTFE (polytetrafluoroethylene) filters using a standard Fmoc protocol. A solution of 20%
piperidine in DMF was used for Fmoc cleavage and, after washing with DMF, the coupling of the following residue was achieved using 4 equiv of acid, HBTU, and HOBt in presence of 8 equiv of DIPEA. The used synthesis cycle is shown in Table 5.2
Table 5.2: Steps of the used standard SPPS cycle.
Step Procedure and reagent Time (min)
1 resin swelling (only for first cycle) 1 10
2 Fmoc cleavage 1 5 and 1 20
3 washing with DMF 1 3 1
4 washing with DMF 2 3 1
5 washing with DMF 3 2 1
6 Fmoc amino acid coupling 1 120
7 washing with DMF 4 3 1
8 washing with DMF 1 1 1
83 Method D
Weak acidic cleavage from resin keeping side chain protections
After completing the SPPS, the peptide was cleaved from the resin using 1% TFA in DCM (3 30 min). The solution containing the cleaved peptide was immediately neutralized with DIPEA after each cleavage step. Finally, the solvents were removed in vacuum.
Method E
Strong acidic cleavage from resin
After completing the SPPS, the peptide was cleaved (approximately 1 h) from resin using a mixture of TFA/TIS/H2O (95/2.5/2.5, v/v/v). For intermediates the solvent was removed in vacuum and used for the next step.
If the desired inhibitor/peptide was obtained at this cleavage, the TFA was partially removed and the remaining solution was added dropwise to cold diethyl ether. The precipitate was obtained by centrifugation, washed with diethyl ether, and dried in vacuum. The product was purified by preparative HPLC, and lyophilized from water or 80% tert-butanol.
Method F
PyBOP coupling99
1 equiv of an amino component and 1 equiv of the carboxyl derivative were dissolved in DMF (5 mL/mmol) and treated with 1 equiv PyBOP and 2-3 equiv DIPEA to reach a pH value between 8.5 and 9.5. The mixture was stirred at 0 °C for 30 minutes and at RT for 2 h. The solvent was removed in vacuum. The residue was dissolved in EtOAc and washed trice with 5% KHSO4-solution, once with brine, trice with saturated NaHCO3 -solution, and trice with brine. The EtOAc phase was dried over Na2SO4, filtered, and the solvent was removed in vacuum.
Method G
Cleavage of Cbz-protecting group by HBr/acetic acid98
1 equiv of Cbz-protected compound was dissolved in 32% HBr in glacial AcOH (10 mL/mmol).The mixture was shaken several times within 1 h at RT. The solvent was partially removed in vacuum and the product was precipitated by diethyl ether, filtered,
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washed with diethyl ether, and dried in vacuum. Alternatively, the product was purified by preparative HPLC, and lyophilized from water or 80% tert-butanol.
Method H
Introduction of Boc protecting group98
1 equiv of the amino acid was dissolved in a mixture of organic solvent (dioxane or acetonitrile) and water (2:1, v/v, 5 mL/mmol) at 0 °C. This mixture was treated with 1.1 equiv 1 N NaOH and 1.1 equiv di-tert-butyl dicarbonate. The pH was adjusted to 8.5-9.5 with 1 N NaOH. The mixture was stirred for 3 h at RT, whereby the reaction was controlled by HPLC. If necessary, an additional amount of (Boc)2O and 1 N NaOH were added and the mixture was further stirred at RT overnight. The solvent was removed in vacuum. The residue was dissolved in EtOAc, washed trice with 5%
KHSO4-solution, and trice with brine. The EtOAc phase was dried over Na2SO4, filtered and removed in vacuum.
Method I
Cleavage of Boc-protecting group by 90% TFA100
1 equiv of Boc-protected compound was dissolved in 90% TFA (5 mL/mmol) and the mixture was stirred for 1 to 2 h at RT. The solvent was removed in vacuum. If the desired inhibitor/peptide was obtained at this step, the TFA was partially removed and the product was precipitated by diethyl ether, filtered, washed with diethyl ether, and dried in vacuum. The product was purified by preparative HPLC, and lyophilized from water or 80% tert-butanol.
Method J
Hydrogenation101
The compound was dissolved in 90% AcOH and treated with approximately 10 mass percent of catalyst (10% Pd/C). The mixture was stirred at least overnight under a hydrogen atmosphere. If necessary (HPLC control), the hydrogenation was continued at RT for additional 24 h. The catalyst was removed by filtration and the solvent was evaporated. Alternatively, the product was purified by preparative HPLC and lyophilized from water or 80% tert-butanol.
85 Method K
Introduction of the Tfa-group 97
1 equiv of the amino component was dissolved in methanol and treated with 1 equiv of trifluoroacetic anhydride and 1equiv of DIPEA. The mixture was stirred at 0 °C for 1 h and at RT for 2 h. The reaction progress was monitored by HPLC, and if necessary, an additional amount of trifluoroacetic anhydride was added and stirring was continued at RT overnight. The solvent was removed in vacuum. The remaining residue was dissolved in EtOAc and washed trice with 5% KHSO4-solution and trice with brine. The EtOAc phase was dried over Na2SO4, filtered and the solvent was removed in vacuum.
Method L
Cleavage of the Tfa-protecting group with 1 N NaOH100
The corresponding Tfa-protected amino derivative was dissolved in a mixture of dioxane and water (1:1, 10 mL/mmol) and the pH was adjusted to 12 using 1 N NaOH.
The mixture was stirred for 3 h (HPLC control), and if necessary, stirring was continued for some hours until the end of the reaction. The solution was neutralized by the addition of 10% TFA and the solvent was removed in vacuum. The product was purified by preparative HPLC and lyophilized from 80% tert-butanol.
Method M
Conversion of amino into guanidino group102
1 equiv of the free amino intermediate was dissolved in DMF (10 mL/mmol), treated with 2 equiv 1H-pyrazole-1-carboxamidine × HCl, and 3 equiv DIPEA. The mixture was stirred at RT for 24 h (HPLC control) and if necessary, an additional amount of 1H-pyrazole-1-carboxamidine × HCl and DIPEA were added, and stirring was continued until completion of the reaction. The solvent was removed in vacuum.
Method N
Conversion of amino into di-Boc-protected guanidino group103
1 equiv of the free amino intermediate was dissolved in DMF (10 mL/mmol), treated with 2 equiv N,N’-di-Boc-1H-pyrazole-1-carboxamidine, and 3 equiv DIPEA. The mixture was stirred at RT for 24 h (HPLC control) and if necessary, an additional
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amount of N,N’-di-Boc-1Hpyrazole-1-carboxamidine and DIPEA were added, and stirring was continued until completion of the reaction. The solvent was removed in vacuum.
Method O
Conversion of amino into methyl/ethyl-guanidine group88
1 equiv of the free amino intermediate was dissolved in DMF (10 mL/mmol), treated with 2 equiv 2-Ethyl-1-methyl-isothiourea hydroiodide or 2-Ethyl-1-ethyl-isothiourea hydroiodide, and 2 equiv DIPEA. The mixture was stirred at RT for 24 h (HPLC control) and if necessary, an additional amount of the guanylation reagent and DIPEA were added, and stirring was continued until completion of the reaction. The solvent was removed in vacuum.
Method P
Introduction of Fmoc protecting group98
1 equiv of the amino derivative was dissolved in ACN (10 mL/mmol) and treated with 2 equiv NMM or DIPEA. 1 equiv Fmoc-OSu dissolved in ACN80 (5 mL/mmol) was added in two portions and the mixture was stirred at 0°C for 1h. The pH value was set to 8.5-9.5 by the addition of NMM or DIPEA. The mixture was stirred at RT for 3 h (HPLC control). If necessary, additional amounts of Fmoc-OSu and NMM or DIPEA were added and the mixture was further stirred at RT overnight. The solvent was removed in vacuum.
Method Q
Intramolecular cyclization in solution89
The peptide containing one free amino and one carboxyl group was dissolved in DMF (100 mL/0.1mmol). The mixture was treated with 3 equiv BOP and initially with 3 equiv DIPEA, followed by stirring at 0°C for 1h. During the reaction the pH was controlled several times and adjusted to 8.5-9.5 by adding small portions of DIPEA.
The mixture was stirred at RT for 48-72 h and the reaction progress was controlled by HPLC. Finally, the solvent was removed in vacuum, the remaining residue was
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dissolved in EtOAc and washed with 5% KHSO4-solution and trice with brine. The EtOAc phase was dried over Na2SO4, filtered, and the solvent was removed in vacuum.