Crystalline dipeptides useful in the synthesis of elamipretide

Abstract

Disclosed are crystalline forms of L-Lys(Boc)-Phe-NH2 and Boc-D-Arg-DMT. The crystalline forms may be used in the synthesis of elamipretide.

Description

BACKGROUND OF THE INVENTION

Elamipretide (MTP-131) is a mitochondria-targeting peptide compound with therapeutic potential for treating diseases associated with mitochondrial dysfunction. Elamipretide contains four-amino acid residues and has been synthesized according to typical linear and convergent solution phase peptide synthesis methods. The synthetic routes to generate elamipretide that have been used to date require the preparation of various differentially protected peptides, such that certain protecting groups are selectively removed in order to subject the deprotected compound to peptide coupling, while other protecting groups remain to prevent unwanted side reactions. Even with protecting groups such coupling reactions and related steps generate impurities. Thus, there exists a need to develop new methods to purify elamipretide that allow the purification after coupling reactions. Crystallization of the desired reaction products are one method of achieving the necessary purification.

SUMMARY OF THE INVENTION

Disclosed are crystalline forms of L-Lys(Boc)-Phe-NH₂ and Boc-D-Arg-DMT, wherein DMT is an abbreviation for dimethyltyrosine, which are intermediates in the synthesis of elamipretide.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is the XRPD pattern of crystalline L-Lys(Boc)-Phe-NH₂. The peak listing of the XRPD pattern depicted in FIG. 1 is described in Table 1.

FIG. 2 is the XRPD pattern crystalline Boc-D-Arg-DMT. The peak listing of the XRPD pattern depicted in FIG. 2 is described in Table 2.

DETAILED DESCRIPTION OF THE INVENTION

Elamipretide has been shown to have various therapeutic effects in diseases related to mitochondrial dysfunction. Previous synthetic routes to elamipretide presented challenges with respect to scale-up due to reliance on chromatographic separations to enrich levels of desired intermediates. Herein are disclosed crystalline forms of L-Lys(Boc)-Phe-NH₂ and Boc-D-Arg-DMT, which can be used as purified intermediates in the synthesis of elamipretide.

One aspect of the present invention relates to crystalline forms of Compound (I):

which compound is also known as L-Lys(Boc)-Phe-NH₂.

A crystalline form of Compound (I) can be used in the synthesis of elamipretide.

In certain embodiments, a polymorph of the crystalline form is characterized by powder X-ray diffraction (XRD). θ represents the diffraction angle, measured in degrees. In certain embodiments, the diffractometer used in XRD measures the diffraction angle as two times the diffraction angle θ. Thus, in certain embodiments, the diffraction patterns described herein refer to X-ray intensity measured against angle 2θ.

In certain embodiments, a crystalline form of Compound (I) is not solvated (e.g., the crystal lattice does not comprise molecules of a solvent). In certain alternative embodiments, a crystalline form of Compound (I) is solvated. In some cases, the solvent is water.

In one aspect, the invention features a crystalline form of Compound (I) which has characteristic peaks in the powder X-ray diffraction (XRPD) pattern as shown in FIG. 1.

In another aspect, the invention features a crystalline form of Compound (I) which has characteristic peaks in the powder X-ray diffraction (XRPD) pattern at values of two theta (° 2θ) as shown in Table 1.

In another aspect, the invention features a crystalline form of Compound (I) which has characteristic peaks in the powder X-ray diffraction (XRPD) pattern at values of two theta (° 2θ) of: 4.7, 6.2, 12.4, 15.8, 16.5, 18.0, 18.2, 18.8, and 19.8.

In another aspect, the invention features a crystalline form of Compound (I) which has characteristic peaks in the powder X-ray diffraction (XRPD) pattern at values of two theta (° 2θ) of: 4.7, 6.2, 11.3, 12.4, 13.3, 15.0, 15.8, 16.5, 17.0, 17.7, 18.0, 18.2, 18.8, 19.8, 22.0, and 22.8.

The relative intensity, as well as the two theta value, of each peak in Table 1, as well as in FIG. 1, may change or shift under certain conditions, although the crystalline form is the same. One of ordinary skill in the art should be able to determine readily whether a given crystalline form is the same crystalline form as described in Table 1, as well as in FIG. 1, by comparing their XRPD data.

One aspect of the present invention relates to a crystalline form of Compound (II):

which compound is also known as Boc-D-Arg-DMT, and may also be drawn in the form of a zwitterion.

A crystalline form of Compound (II) can be used in the synthesis of elamipretide.

In certain embodiments, a polymorph of the crystalline form is characterized by powder X-ray diffraction (XRD). θ represents the diffraction angle, measured in degrees. In certain embodiments, the diffractometer used in XRD measures the diffraction angle as two times the diffraction angle θ. Thus, in certain embodiments, the diffraction patterns described herein refer to X-ray intensity measured against angle 2θ.

In certain embodiments, a crystalline form of Compound (II) is not solvated (e.g., the crystal lattice does not comprise molecules of a solvent). In certain alternative embodiments, a crystalline form of Compound (II) is solvated. In some cases, the solvent is water.

In one aspect, the invention features a crystalline form of Compound (II) which has characteristic peaks in the powder X-ray diffraction (XRPD) pattern as shown in FIG. 2.

In another aspect, the invention features a crystalline form of Compound (II) which has characteristic peaks in the powder X-ray diffraction (XRPD) pattern at values of two theta (° 2θ) as shown in Table 2.

In another aspect, the invention features a crystalline form of Compound (II) which has characteristic peaks in the powder X-ray diffraction (XRPD) pattern at values of two theta (° 2θ) of: 9.3, 12.1, 16.6, 17.6, 18.0, 18.8, and 19.4.

In another aspect, the invention features a crystalline form of Compound (II) which has characteristic peaks in the powder X-ray diffraction (XRPD) pattern at values of two theta (° 2θ) of: 9.3, 12.1, 13.7, 16.3, 16.6, 17.6, 18.0, 18.8, 19.4, 21.3, 23.0, 24.2, and 25.1.

The relative intensity, as well as the two theta value, of each peak in Table 2, as well as in FIG. 2, may change or shift under certain conditions, although the crystalline form is the same. One of ordinary skill in the art should be able to determine readily whether a given crystalline form is the same crystalline form as described in Table 1, as well as in FIG. 1, by comparing their XRPD data.

EXAMPLES

Materials and Methods

Name                  RM0858 General Method (2607)
Parent                2Theta
Sample Name           S-18-0011882 SCC-169
File Name             RM0858 General Method (2607)
Scan Type             Coupled TwoTheta/Theta
Scan Mode             Continuous PSD fast
Start                 2.000
End                   40.016
Step Size             0.050
Time per Step         192.00
Anode                 Cu
kα1                   1.54
Generator kV          40.0
Generator mA          40.0
PSD Opening           2.940
Detector Slit Opening
Primary Soller slit   2.500
Secondary Soller slit 2.500
Sample rotation speed 15.000
Divergence Slit       0.600
Antiscatter Slit      3.000
Slit Mode             Fixed

Example 1. L-Lys(Boc)-Phe-NH2 (Compound I)

Exemplary Synthetic Route

Synthesis of Compound 3

							BR
	Amount	Volume	MW	Molar		Density	Charge
Name	(g)	(mL)	(g/mol)	Equiv	Moles	g/mL	Amt (kg)	kg/kg
Phe-NH2 HCl	950.00	950.00	200.67	1.00	4.734	—	7.030
Cbz-Lys(Boc)-OH	1891.11	1891.11	380.44	1.05	4.971	—	13.990	1.99
HOBt-H2O	797.48	797.48	153.14	1.10	5.208	—	5.900	0.84
Dimethylacetamide	3736.49	3987.71	87.12	—	—	0.937	27.650	3.93
(DMAc)
N-	957.72	1041.00	101.15	2.00	9.468	0.920	7.080	1.01
Methylmorpholine
(NMM)
EDCI	952.91	952.91	191.70	1.05	4.971	—	7.050	1.00
Anhydrous Ethyl	750.50	951.20	46.07	—	—	0.789	5.550	0.79
Alcohol (EtOH)
Acetonitrile (ACN)	11202.70	14252.80	84.93	—	—	0.786	82.900	11.79
Acetonitrile (ACN)	11202.70	14252.80	85.93	—	—	0.786	82.900	11.79

	Operation	Charge	Units
	Inert the reactor with nitrogen.
1	Charge Compound 1 to reactor.	950.00	g
2	Charge Compound 2 to reactor.	1891.11	g
3	Charge HOBt-H2O to reactor.	797.48	g
4	Charge DMAc to reactor.	3736.49	g
5	Adjust solution to target 22° C. (19 to 25° C.)
	with agitation.
6	Agitate for 10-15 min at 22° C. (19 to 25° C.).
7	Slowly charge NMM to reactor with moderate	957.72	g
	agitation.
8	Adjust solution to target 7° C. (4 to 10° C.)
	with agitation.
9	Slowly charge EDCI to reactor with vigorous	952.91	g
	agitation.
10	Adjust solution to target 7° C. (4 to 10° C.)
	with vigorous agitation.
11	Charge EtOH to reactor with vigorous	750.50	g
	agitation.
12	Adjust solution to target 22° C. (19 to 25° C.)
	with vigorous agitation.
13	Agitate vigorously for ≥1 h at 22° C. (19 to
	25° C.).
	IPC for Reaction Completion (≤1.0% Phe-	0.169% a/a
	NH2 remaining)
CRYSTALLIZATION
15	Charge ACN to the reactor with vigorous	11202.70	g
	agitation.
16	Agitate vigorously for ≥5 h at 22° C. (19 to
	25° C.).
17	Verify crystallization successful.
18	Filter the reaction to isolate the product
	(SCC-175).
19	Wash the product cake with ACN and combine	11202.70	g
	with mother liquor.
20	Dry the product with agitation and nitrogen
	bleed for at least 17 h.

Synthesis of Compound I

						BR
		Volume	MW	Molar	Density	Charge
Name	Amt	(mL)	(g/mol)	Equiv	g/mL	Amt	units	kg/kg
Compound 3	2000.00	2000.00	526.63	1.00		15.700	kg
10% Pd/C (50%	200.00	200.00	106.42	10%	—	3.140	kg	0.20
w/w wet)				w/w
Anhydrous	14191.08	17918.03	32.04	—	0.792	111.400	kg	7.10
Methyl Alcohol
(MeOH)
Anhydrous	7000.00	8838.38	32.04	—	0.792	54.950	kg	3.50
Methyl Alcohol
(MeOH)
Water	7000.00	7000.00	18.02		1.000	54.950	kg	3.50
Water	8000.00	8000.00	18.02		1.000	62.800	kg	4.00
MeOH-Water	8000.00	7896.00			0.987	62.800	kg	4.00
(1:9) Solution
Water (1:9	9000.00	9000.00	18.02		1.000	NA		NA
MeOH-water
make-up)
Anhydrous	792.00	1000.00	33.04	—	0.792	NA		NA
Methyl Alcohol
(MeOH) (1:9
MeOH-water
make-up)

	Operation	Charge	Units
	REACTION (30 L Hydrogenator Main Reactor)
	Inert the hydrogenation reactor with nitrogen.
1	Charge Pd/C (10%, 50% w/w water, 20A597) to	200.00	g
	reactor.
2	Charge Compound 3 to reactor.	2000.00	g
3	Charge MeOH to the reactor.	14191.08	g
4	Adjust solution to target 22° C. (19 to 25° C.)
	with agitation.
	Inert the hydrogenation reactor with nitrogen.
5	Pressurize the reactor with hydrogen (20-25 psi).
6	Agitate for ≥6 h at 22° C. (19 to 25° C.) and
	20-25 psi hydrogen.
	Note: Maintain the pressure at 20-25 psi
	hydrogen.
7	De-pressurize the reactor and inert with nitrogen
	at 22° C. (19 to 25° C.).
	IPC for Reaction Completion (≤0.5% SCC-175	0.09% a/a
	remaining)
9	Filter the reaction to remove catalyst.
10	Rinse the filter cake with MeOH and combine	7000.00	g
	with filtrate.
	DISTILLATION (30 L ChemGlass Jacketed Main
	Reactor)
11	Distill the reaction at ≤45° C. (100-200 Torr
	vacuum) to target.
	Note: Distillation target = 1.5-2.5 mL/g SCC-	5000.00	mL
	175 charge.
	PRECIPITATION (30 L ChemGlass Jacketed
	Main Reactor)
	ISOLATION (12 L Allen Glass Filter w/30
	micron ChemGlass teflon frit)
12	Charge water to reactor with moderate agitation	7000.00	g
	at 40° C. over 30-60 min.
13	Agitate the reaction at at 40° C. until
	crystallization observed.
14	Verify crystallization successful.
15	Charge water to reactor with moderate agitation	8000.00	g
	at 40° C. over 30-60 min.
16	Adjust the reaction to 22° C. (20 to 25° C.) over
	30-60 min.
17	Filter the reaction to isolate the product (SCC-
	169).
18	Wash the product cake with MeOH-water (1:9).	8000.00	g
19	Dry the product with agitation and nitrogen
	bleed for at least 17 h.

Preliminary Single-Solvent Solubility of Compound I:

Solvent       Solubility (mg/mL)A
EtOH (SDAG-7) 154.8
THF           84.5
iPrOAc        5.1
MeOAc         18.2
Water         4.1
ASolubility was determined by HPLC (response curve).

Preliminary Precipitation Studies (MeOH/Water) of Compound I:

Precipitation Studies
	MeOH/	Addition	Precip	Concentration	Solubility
Experiment	Water	Mode	(Y/N)	(mL/g)	(mg/mL)
1A	1:3	Normal	Y	10	7.0
2A	1:5	Normal	Y	10	5.0
3A	1:9	Normal	Y	10	3.6
4A	1:19	Normal	Y	10	2.7
5B	1:3	Reverse	N	80	—
+2 parts	1:5	Normal	Y	120	ND
water
AExperiments were conducted on 500 mg scale where the initial solution in MeOH (via 2447-41) was concentrated to a residue followed by charging MeOH/water at 25° C.
BExperiment was conducted on 40 mg scale where the initial solution in MeOH (via 2447-41) was charged directly to water. An additional charge of water was required to enable precipitation.

In Process Precipitation Results (MeOH/Water) of Compound I:

Precipitation Results
		Concentration	Solubility
Experiment	MeOH/Water	(mL/g)	(mg/mL)	Total Losses
2447-41A	1:9	13	2.5	5.7%
2447-47A	1:5	10	4.2	6.2%

Example 2. Boc-D-Arg-DMT-OH

Manufacturing Process to Produce Compound 8

Step Operation
1    Charge DMT-OBn HCl (1 eq) and Boc-D-Arg-OH HCl (1.05 eq)
     to the reactor.
2    Charge HOBt (0.1 eq) and DCM (8.5 L/kg of DMT-OBn HCl)
     to the reactor.
3    Adjust temperature to about 22 ± 3° C. and charge NMM
     (2.0 eq) to the reactor
4    Adjust temperature to about 15 ± 3° C. and charge EDCI
     (1.05 eq) to the reactor.
5    Adjust temperature to about 15° C. and agitate.
5    Charge EtOH (1.5 L/kg of DMT-OBn HCl) to the reactor
7    Agitate for a minimum of 5 hours at 15 ± 3° C.
8    Sample for in-process control reaction completion test, if
     reaction is not complete, charge additional EDCI, stir for
     a minimum of 1 hour andrepeat the in-process control test
     until criterion for completion is met.
9    Charge 15% EtOH in DCM.
10   Charge 1M HCl.
11   Adjust temperature to ambient and agitate.
12   Stop agitation and separate layers
13   Wash organic layer successively with brine, 1M HCl, brine
     and then brine again
14   Reduce volume via vacuum distillation
15   Adjust temperature to ambient
16   Charge EtOH and reduce volume via vacuum distillation
17   Sample for in-process control DCM content test, Repeat EtOH
     addition and volume reduction by vacuum distillation until
     the in-process control limit for DCM is met
18   Adjust temperature to ambient
19   Sample the product for in-process control test for SCC-192
     purity and content

Manufacturing Process to Produce the HCl Salt of Compound II

Step Operation
1    Charge the ethanol solution of Boc-D-Arg-DMT-OBn HCl
     (SCC-192)
2    Charge 10% Pd/C, 50% wet (w/w) (20 wt. %)
3    Charge EtOH (7 L/kg of SCC-192)
4    Agitate and begin hydrogenation around ambient
     temperature
5    Step 2B In-Process Control 1: Test for reaction
     completion
5    Filter suspension through filter aid and wash filter
     cake three times with EtOH
7    Reduce volume via vacuum distillation
8    Adjust temperature to ambient
9    Charge THF and reduce volume via vacuum distillation
10   Adjust temperature to ambient
11   Charge THF and reduce volume via vacuum distillation
12   Adjust temperature to ambient
13   Charge THF and reduce volume via vacuum distillation
14   Step 2B In-Process Control 2: Test for EtOH content
15   Charge iPrOAc and agitate at ambient temperature
16   Filter and wash solids three times with iPrOAc
17   Dry the product under vacuum and nitrogen
18   Sample the product for in-process control test for
     purity
19   Step 2B In-Process Control 3: Test for Purity

Preparation of the Zwitterionic Form of Compound II

• • 1. The crude HCl salt is suspended in CH₃OH/H₂O (l/l, v/v)
  • 2. The suspension is heated to 45-50° C.
  • 3. After the clear solution is formed, an aqueous solution of Na₂CO₃ (1.2 eq.) is added. During the addition, the solid begins to precipitate.
  • 4. The suspension is stirred for 1 h at 45° C., and then cooled to 15° C. and stirred for an additional hour.
  • 5. The solid is isolated by filtration and dried to provide Compound II with high purity (99.4 area %) by HPLC. The calculated w/w assay correcting for residual solvents, water content and residue on ignition for this demonstration run was 98.7%.

Formation of zwitterionic compound led to high purity material that was stable, easily handled, and highly crystalline.

Example 3. Crystalline L-Lys(Boc)-Phe-NH₂-XRPD Peak List (Table 1)

Angle	d Value	Net Intensity	Gross Intensity	Rel. Intensity
4.704	18.77211	9559	11528	100.0%
5.230	16.88407	624	2301	6.5%
5.648	15.63394	862	2340	9.0%
6.200	14.24402	7663	8912	80.2%
6.650	13.28067	394	1456	4.1%
7.056	12.51772	508	1400	5.3%
7.709	11.45860	1161	1869	12.1%
8.553	10.33046	2135	2771	22.3%
9.402	9.39869	2473	3073	25.9%
9.922	8.90729	2627	3206	27.5%
10.303	8.57920	1435	1997	15.0%
11.292	7.82975	3301	3848	34.5%
11.755	7.52244	1985	2530	20.8%
12.265	7.24594	2827	3370	29.6%
12.452	7.10258	4581	5123	47.9%
12.655	6.98916	2764	3305	28.9%
13.270	6.66655	4117	4655	43.1%
13.778	6.42221	795	1330	8.3%
14.133	6.26164	333	866	3.5%
14.462	6.11961	882	1413	9.2%
14.957	5.91833	3726	4255	39.0%
15.756	5.61997	7404	7928	77.5%
16.263	5.44580	2360	2881	24.7%
16.504	5.36683	5366	5885	56.1%
16.961	5.22337	2930	3447	30.7%
17.107	5.17917	2585	3100	27.0%
17.658	5.01859	3807	4320	39.8%
17.956	4.93596	4360	4871	45.6%
18.210	4.86777	4451	4960	46.6%
18.832	4.70852	8963	9468	93.8%
19.561	4.53460	3331	3830	34.8%
19.802	4.47996	7877	8375	82.4%
20.265	4.37865	1989	2483	2.8%
20.715	4.28449	1746	2237	18.3%
21.514	4.12715	1756	2241	18.4%
21.958	4.04471	4087	4568	42.7%
22.807	3.89590	3856	4331	40.3%
23.398	3.79891	779	1248	8.1%
23.660	3.75740	835	1303	8.7%
24.306	3.65896	726	1188	7.6%
25.050	3.55198	2158	2614	22.6%
25.462	3.49548	764	1217	8.0%
25.709	3.46234	1227	1677	12.8%
26.016	3.42222	714	1161	7.5%
26.319	3.38357	521	966	5.5%
26.713	3.33445	662	1103	6.9%
27.411	3.25119	709	1143	7.4%
28.356	3.14493	831	1256	8.7%
28.808	3.09564	340	761	3.6%
30.662	2.91341	740	1142	7.7%
61.492	2.83854	649	1041	6.8%
35.876	2.50109	376	740	3.9%
36.369	2.46832	362	723	3.8%

Example 4. Crystalline Boc-D-Arg-DMT-XRPD Peak List (Table 2)

Angle	d Value	Net Intensity	Gross Intensity	Rel. Intensity
8.253	10.70448	3779	4204	15.0%
9.353	9.44784	20863	21225	82.9%
12.104	7.30592	20016	20338	79.6%
12.809	6.90584	2797	3120	11.1%
13.755	6.43269	11432	11758	45.4%
15.709	5.53659	906	1235	3.6%
16.307	5.43127	7500	7829	29.8%
16.556	5.35006	12773	13103	50.8%
16.725	5.29645	2495	2825	9.9%
17.557	5.04740	22493	22824	89.4%
18.006	4.92236	25154	25485	100.0%
18.756	4.72740	18203	18534	72.4%
18.908	4.68953	4809	5141	19.1%
19.414	4.56848	12725	13056	50.6%
20.715	4.28417	899	1231	3.6%
21.259	4.17597	5674	5406	20.2%
22.357	3.97329	3830	4161	15.2%
23.009	3.86218	7511	7842	29.9%
23.153	3.83695	2203	2533	8.8%
23.511	3.78085	4659	4989	18.5%
24.208	3.57354	7257	7585	28.8%
24.809	3.58598	1940	2268	7.7%
25.060	3.55054	5627	5954	22.4%
25.767	3.45478	970	1297	3.9%
26.009	3.42308	1418	1744	5.6%
26.457	3.36613	255	580	1.0%
26.721	3.33347	161	485	0.6%
27.763	3.21973	1852	2185	7.4%
28.111	3.17181	1182	1503	4.7%
28.263	3.15505	366	687	1.5%
29.111	3.06507	2546	2864	10.1%
29.311	3.04456	1100	1418	4.4%
29.652	3.00931	616	933	2.4%
29.912	2.98475	1550	1865	6.2%
30.212	2.95583	1607	1922	6.4%
30.865	2.89475	1913	2226	7.6%
31.414	2.84540	1565	1876	6.2%
31.695	2.82084	468	778	1.9%
32.665	2.73926	657	963	2.6%
32.915	2.71901	296	602	1.2%
33.805	2.64939	326	632	1.3%
34.165	2.62230	670	976	2.7%
34.977	2.56330	485	795	1.9%
36.166	2.48167	798	1113	3.2%
36.514	2.45883	611	927	2.4%
36.813	2.43955	364	682	1.4%
37.466	2.39651	173	502	0.7%
37.966	2.36808	901	1257	3.6%
38.221	2.35285	394	764	1.6%
38.576	2.33202	878	1265	3.5%
39.114	2.30117	394	810	1.6%
39.516	2.27866	363	801	1.4%

INCORPORATION BY REFERENCE

All U.S. patents and U.S. and PCT published patent applications mentioned in the description above are incorporated by reference herein in their entirety.

EQUIVALENTS

Having now fully described the present invention in some detail by way of illustration and examples for the purposes of clarity of understanding, it will be obvious to one of ordinary skill in the art that the same can be performed by modifying or changing the invention within a range of conditions, formulations and other parameters without affecting the scope of the invention or any specific embodiment thereof, and that such modifications or changes are intended to be encompassed within the scope of the appended claims.

Claims

1. A crystalline form of Compound (I),

2. A crystalline form of Compound (I),

3. A crystalline form of Compound (I),

4. The crystalline form of claim 3, wherein said crystalline form has characteristic peaks in its XRPD pattern at values of two theta (° 20) of: 4.7, 6.2, 11.3, 12.4, 13.3, 15.0, 15.8, 16.5, 17.0, 17.7, 18.0, 18.2, 18.8, 19.8, 22.0, and 22.8.