A novel oxazolidinone anti­biotic: RWJ-416457

The crystal structure of the anti­biotic drug candidate RWJ-416457 (systematic name: N-{(5S)-3-[4-(5,6-dihydro-2H,4H-2-methylpyrrolo[3,4-c]pyrazol-5-yl)-3-fluorophenyl]-2-oxo-1,3-oxazolidin-5-yl}acetamide), C₁₈H₂₀FN₅O₃, which belongs to the first new class of anti­biotics discovered in the past 30 years, has been determined at 150 K. Each mol­ecule of this drug donates one hydrogen bond to a neighboring mol­ecule and accepts one hydrogen bond to give (O=C—R—N—H...O=C—R—N—H...)_n linkages along the b-axis direction. The compound contains a pyrrolopyrazole ring, which, owing to its uncommon structure, has been shown to have particular effectiveness against multi-drug-resistant bacteria.

S1. Comment

The title compound, RWJ-416457, (I) (Foleno et al., 2007), belongs to the oxazolidinone class of compounds, which are the first new class of antibiotics in the past 30 years (Dresser & Rybak, 1998). Compound (I) is a novel antibiotic drug candidate which inhibits the growth of Gram-positive clinical pathogens, including health-care-associated methicillin-resistant Staphylococcus aureus (MRSA). Although prone to oxidation in aqueous solution, (I) is stable to oxidation as a crystalline solid. Compound (I) degrades via an oxidative mechanism in solution to give ring-opened species of the pyrrolopyrazole. The degradation is enhanced at lower pH and in the presence of metals such as copper and iron. Particular care was taken during characterization of the drug substance to analyze for trace metals. Crystals of the title compound were grown from a mixture of dimethyl sulfoxide (DMSO) and water.

Compound (I) has two carbonyl O atoms that can serve as hydrogen-bond acceptors and one secondary amide N atom that can act as a hydrogen-bond donor. It is found in the crystal structure that each molecule of (I) donates one N—H hydrogen bond to a neighbouring molecule and accepts one hydrogen bond. Together, the intermolecular interactions form (O═C—R—N—H···O ═C—R—N—H···)_n linkages along the b-axis direction. The urethane carbonyl group of the oxazolidinone ring accepts the N—H hydrogen bond; the secondary amide carbonyl group is not involved in hydrogen bonding. There is no evidence of F···F short contacts, or C–H···π or π–π interactions between the aromatic rings.

Compound (I) is optically pure from the chemical synthesis, being assembled from enantiopure chiral starting material of the oxazolidinone ring (S configuration at the lone chiral centre on the molecule). This oxazolidinone ring is known to be a key component of the antibacterial properties of the compound. Unique to compound (I) is its pyrrolopyrazole ring system. A search of the Cambridge Structural Database (CSD; Version 1.11 of September 2009; Allen, 2002) for the pyrrolopyrazole ring system indicated that this moiety has not been previously characterized structurally. The rarity of this ring system is a likely contributor to the effectiveness of the molecule in combating bacteria that show resistance to other treatments (Foleno et al., 2007). This bicyclic eight-membered ring is also highly reactive, as observed from its solution chemistry in which ring opening occurs when the N1—C7 or N1—C10 bonds break. The degradation products are reactive aldehydes, which are susceptible to nucleophilic addition. Within living cells, the presence of aldehydes is undesirable, and these degradation products may alter the antibacterial nature of the compound.

One key observation for compound (I) is its long-term chemical stability as a crystalline material compared with its short solution half-life. The layers of hydrogen-bonded molecules likely act as protective barriers against oxygen attack on the bicyclic ring. Large-scale molecular motions are also forbidden in the solid state, so the cleavage of the pyrrolopyrazole ring and rearrangement to the aldehydes is less favourable. The molecule is free of such contraints in solution, resulting in rapid degradation of the compound.

The crystalline form of this compound provides further stability because of its low solubility in water. At 5.8 ng ml^-1, the equilibrium solubility does not allow for significant amounts of compound to be in solution at any given time. Dissolved drug substance is a requirement for the solution-mediated degradation pathway. The crystalline drug has a further advantage because crystallization also acts as a purification step in removing metals and acid, which can persist beyond the final synthetic step, causing degradation of the drug candidate during its shelf-life. In light of the solution deficiencies of this compound, the drug in its crystalline form is therefore essential for stable storage as a drug candidiate in the clinic.

Related literature

For related literature, see: Allen (2002); Betteridge et al. (2003); Dresser & Rybak (1998); Foleno et al. (2007); Spek (2009).

S2. Experimental

RWJ-416457 (75.4 mg; 0.20 mol) was added to DMSO (1 ml, 0.63 mol) in water at 353 K. Malonic acid (1.186 g, 11.39 mol) was added to the solution to increase the solubility of (I). The solution of (I) and malonic acid was passed through a 0.2 µm filter and the filtrate was left to cool in a glass vial at room temperature. Single crystals of the title compound appeared after 1 d.

S3. Refinement

Structure determination of (I) was initiated in space group P2₁ as indicated from the observed metric constants, intensity statistics and systematic absences. Subsequent structure solution and refinement confirmed this choice; however, least-squares refinement failed to improve R1 < 17% for F² > 2σ(F²). Twinning was suspected, and close inspection of the frames for the full data collection revealed a number of extra reflections that did not overlap with the original unit cell. Domain searching analysis using ROTAX (Cooper et al., 2002) revealed a twin law [0.998 0 -0.005/0 -1 0/ -0.999 0 -0.998] as well as an optimized `twin tolerance' parameter of 0.022 Å^-1, which identified the overlapping and separate reflections from the two domains (Cooper et al., 2002). The analysis and successful refinement demonstrated that the crystal was a twin lattice quasi-symmetry twin (Donnay & Donnay, 1974; Giacovazzo, 1992) with a rotation about [102] and small twin obliquity (Donnay & Donnay, 1972), ω = 0.46^o. Scale factors for the two twin components were constrained to sum to 1.0, with the value of the major twin component scale refining to 0.8037 (17). Least-squares refinement of the data on F² using this twin law led to significant improvement [R1 = 4.9% for F² > 2σ(F²)]. In an attempt to improve the data, CELL_NOW (Sheldrick, 2003) was run on the original data, yielding a numerically identical twin law. The data were integrated using the two-domain .p4p file, and TWINABS (Sheldrick, 2002) was used to generate HKLF4 and HKLF5 files. The refinement using these files was not significantly different, with marginally higher R vales, from that using the ROTAX procedure described above, and thus the original refinement was retained. The molecules are ordered and closely packed (Kitaigorodskii packing index KPI = 71.4%) (Spek, 2009).

All non-H atoms were refined using anisotropic displacement parameters. After location on an electron density difference map, the H atoms were first regularized with the use of restraints and subsequently allowed to ride on the corresponding C or N atoms, with C—H distances in the range 0.93–0.98 Å and N—H distances of 0.86 Å [0.92–1.00 and 0.87 Å according to CIF].

Computing details

Data collection: APEX2 (Bruker, 2006); cell refinement: APEX2 (Bruker, 2006); data reduction: APEX2 (Bruker, 2006); program(s) used to solve structure: SHELXS86 (Sheldrick, 2008); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: DIAMOND (Crystal Impact, 2009); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures

	Fig. 1. A view of the molecule of (I), showing the atom-numbering scheme. Anisotropic displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.
	Fig. 2. Hydrogen bonding in the RWJ-416457 crystal, forming a simple linear motif [graph set C(7)].

N-{(5S)-3-[4-(5,6-dihydro-2H,4H-2- methylpyrrolo[3,4-c]pyrazol-5-yl)-3-fluorophenyl]-2-oxo-1,3- oxazolidin-5-yl}acetamide

Crystal data

C18H20FN5O3	F(000) = 392
Mr = 373.39	Dx = 1.444 Mg m^−3
Monoclinic, P21	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2yb	Cell parameters from 1377 reflections
a = 4.8358 (17) Å	θ = 2–22°
b = 10.293 (4) Å	µ = 0.11 mm^−1
c = 17.403 (6) Å	T = 150 K
β = 97.524 (10)°	Acicular, colourless
V = 858.7 (5) Å^3	0.31 × 0.04 × 0.01 mm
Z = 2

Data collection

Area diffractometer	1180 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.041
ϕ & ω scans	θmax = 26.0°, θmin = 2.3°
Absorption correction: multi-scan (APEX2; Bruker, 2006)	h = −6→5
Tmin = 1.00, Tmax = 1.00	k = −12→11
5186 measured reflections	l = −22→21
1725 independent reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.049	H-atom parameters constrained
wR(F^2) = 0.087	Method = Modified Sheldrick w = 1/[σ^2(F^2) + (0.02P)^2 + 0.59P], where P = [max(Fo^2,0) + 2Fc^2]/3
S = 0.96	(Δ/σ)max = 0.001
1725 reflections	Δρmax = 0.52 e Å^−3
245 parameters	Δρmin = −0.49 e Å^−3
1 restraint

Special details

Experimental. Data collection: Data collection, integration, scaling, and absorption corrections were carried out using the Bruker Apex2 software (Bruker AXS, 2006). Refinement (full-matrix-least squares) was performed using the Oxford University Crystals for Windows software (Betteridge et al., 2003).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
F1	0.6810 (8)	0.4098 (4)	0.6734 (2)	0.0489
O1	0.1398 (9)	0.4902 (4)	0.8753 (2)	0.0366
O2	0.0443 (8)	0.6627 (4)	0.9470 (2)	0.0306
O3	0.2756 (9)	0.5529 (4)	1.1278 (2)	0.0415
N1	1.0014 (11)	0.6160 (5)	0.6173 (3)	0.0263
N2	1.3050 (11)	0.4938 (5)	0.4523 (3)	0.0358
N3	1.4481 (11)	0.5937 (5)	0.4255 (3)	0.0299
N4	0.3617 (9)	0.6869 (5)	0.8651 (3)	0.0249
N5	0.1920 (10)	0.7670 (5)	1.1065 (3)	0.0283
C1	0.6851 (13)	0.5326 (6)	0.7062 (3)	0.0272
C2	0.8437 (11)	0.6298 (6)	0.6780 (3)	0.0250
C3	0.8335 (12)	0.7489 (6)	0.7177 (3)	0.0268
C4	0.6748 (11)	0.7675 (6)	0.7777 (3)	0.0260
C5	0.5189 (11)	0.6654 (6)	0.8024 (3)	0.0215
C6	0.5250 (12)	0.5458 (6)	0.7654 (4)	0.0268
C7	1.0134 (13)	0.4999 (6)	0.5695 (3)	0.0295
C8	1.2000 (12)	0.5472 (6)	0.5127 (4)	0.0248
C9	1.2786 (11)	0.6748 (6)	0.5253 (3)	0.0267
C10	1.1540 (13)	0.7292 (6)	0.5928 (3)	0.0316
C11	1.4414 (13)	0.7028 (6)	0.4682 (3)	0.0318
C12	1.6037 (13)	0.5757 (7)	0.3594 (4)	0.0404
C13	0.3350 (13)	0.8157 (6)	0.8974 (3)	0.0295
C14	0.1706 (12)	0.7899 (6)	0.9653 (4)	0.0296
C15	0.3518 (12)	0.7833 (6)	1.0429 (3)	0.0305
C16	0.1579 (12)	0.6533 (6)	1.1425 (3)	0.0264
C17	−0.0372 (12)	0.6606 (7)	1.2047 (3)	0.0370
C25	0.1838 (12)	0.6025 (7)	0.8928 (3)	0.0267
H31	0.9483	0.8223	0.7036	0.0330*
H41	0.6719	0.8457	0.8025	0.0325*
H51	0.0992	0.8340	1.1188	0.0338*
H61	0.4256	0.4746	0.7814	0.0317*
H71	0.8279	0.4752	0.5435	0.0363*
H72	1.0940	0.4284	0.6015	0.0355*
H101	1.2955	0.7595	0.6349	0.0364*
H102	1.0268	0.8006	0.5778	0.0359*
H111	1.5284	0.7808	0.4596	0.0396*
H121	1.5274	0.5040	0.3291	0.0618*
H122	1.5910	0.6543	0.3286	0.0611*
H123	1.7939	0.5540	0.3783	0.0615*
H131	0.2347	0.8730	0.8588	0.0370*
H132	0.5157	0.8533	0.9137	0.0368*
H141	0.0236	0.8563	0.9675	0.0343*
H151	0.4811	0.7077	1.0433	0.0367*
H152	0.4587	0.8644	1.0512	0.0361*
H171	−0.0631	0.7493	1.2200	0.0570*
H172	−0.2160	0.6253	1.1848	0.0575*
H173	0.0451	0.6122	1.2500	0.0571*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
F1	0.071 (3)	0.023 (2)	0.055 (3)	−0.0084 (19)	0.018 (2)	−0.0093 (19)
O1	0.038 (3)	0.022 (3)	0.048 (3)	−0.014 (2)	−0.002 (2)	0.002 (2)
O2	0.028 (2)	0.031 (3)	0.033 (2)	−0.011 (2)	0.003 (2)	0.000 (2)
O3	0.052 (3)	0.019 (3)	0.055 (3)	0.015 (2)	0.016 (3)	0.008 (2)
N1	0.032 (3)	0.018 (3)	0.029 (3)	−0.004 (2)	0.004 (3)	−0.004 (2)
N2	0.042 (3)	0.032 (4)	0.035 (3)	−0.008 (3)	0.010 (3)	−0.005 (3)
N3	0.034 (3)	0.030 (4)	0.028 (3)	0.005 (3)	0.008 (3)	0.000 (3)
N4	0.025 (3)	0.019 (3)	0.029 (3)	−0.002 (3)	0.000 (3)	0.001 (2)
N5	0.036 (3)	0.018 (3)	0.032 (3)	0.009 (2)	0.010 (3)	0.001 (3)
C1	0.032 (4)	0.016 (4)	0.033 (4)	0.003 (3)	−0.002 (3)	−0.003 (3)
C2	0.018 (3)	0.026 (4)	0.029 (4)	0.002 (3)	−0.004 (3)	0.002 (3)
C3	0.026 (3)	0.022 (4)	0.031 (3)	−0.001 (3)	−0.002 (3)	0.002 (3)
C4	0.027 (3)	0.018 (4)	0.033 (4)	−0.001 (3)	0.001 (3)	−0.004 (3)
C5	0.022 (3)	0.020 (3)	0.022 (3)	−0.002 (3)	−0.001 (3)	0.003 (3)
C6	0.023 (3)	0.018 (3)	0.037 (4)	0.001 (3)	−0.007 (3)	0.006 (3)
C7	0.032 (4)	0.016 (3)	0.040 (4)	0.004 (3)	0.005 (3)	0.002 (3)
C8	0.023 (3)	0.020 (4)	0.030 (4)	0.003 (3)	0.001 (3)	0.003 (3)
C9	0.023 (3)	0.023 (4)	0.034 (4)	0.006 (3)	0.002 (3)	−0.002 (3)
C10	0.026 (4)	0.031 (4)	0.037 (4)	0.000 (3)	0.003 (3)	−0.004 (3)
C11	0.032 (4)	0.023 (4)	0.040 (4)	0.008 (3)	0.003 (4)	0.004 (3)
C12	0.039 (4)	0.046 (5)	0.037 (4)	0.002 (4)	0.009 (4)	0.000 (3)
C13	0.029 (4)	0.026 (4)	0.034 (4)	−0.003 (3)	0.006 (3)	0.002 (3)
C14	0.027 (3)	0.024 (4)	0.038 (4)	−0.004 (3)	0.005 (3)	0.008 (3)
C15	0.030 (3)	0.029 (4)	0.034 (4)	−0.003 (3)	0.009 (3)	−0.004 (3)
C16	0.020 (3)	0.028 (4)	0.030 (4)	0.000 (3)	0.000 (3)	0.001 (3)
C17	0.035 (4)	0.044 (4)	0.033 (4)	0.005 (4)	0.009 (3)	0.008 (4)
C25	0.018 (3)	0.027 (4)	0.033 (4)	−0.003 (3)	−0.007 (3)	0.009 (3)

Geometric parameters (Å, º)

F1—C1	1.386 (7)	C5—C6	1.392 (8)
O1—C25	1.206 (7)	C6—H61	0.939
O2—C14	1.463 (7)	C7—C8	1.504 (8)
O2—C25	1.377 (7)	C7—H71	0.984
O3—C16	1.224 (7)	C7—H72	0.973
N1—C2	1.388 (7)	C8—C9	1.378 (8)
N1—C7	1.462 (7)	C9—C10	1.498 (8)
N1—C10	1.472 (7)	C9—C11	1.376 (8)
N2—N3	1.356 (7)	C10—H101	0.986
N2—C8	1.343 (7)	C10—H102	0.972
N3—C11	1.348 (7)	C11—H111	0.928
N3—C12	1.466 (7)	C12—H121	0.953
N4—C5	1.426 (7)	C12—H122	0.968
N4—C13	1.453 (7)	C12—H123	0.961
N4—C25	1.355 (7)	C13—C14	1.530 (8)
N5—C15	1.440 (7)	C13—H131	0.975
N5—C16	1.347 (7)	C13—H132	0.963
N5—H51	0.865	C14—C15	1.512 (7)
C1—C2	1.388 (8)	C14—H141	0.991
C1—C6	1.374 (8)	C15—H151	0.997
C2—C3	1.412 (8)	C15—H152	0.982
C3—C4	1.388 (8)	C16—C17	1.528 (7)
C3—H31	0.987	C17—H171	0.964
C4—C5	1.393 (8)	C17—H172	0.959
C4—H41	0.915	C17—H173	0.972
C14—O2—C25	108.9 (4)	C9—C10—H101	113.0
C2—N1—C7	125.6 (5)	N1—C10—H101	111.1
C2—N1—C10	119.1 (5)	C9—C10—H102	112.2
C7—N1—C10	115.0 (4)	N1—C10—H102	110.6
N3—N2—C8	102.8 (5)	H101—C10—H102	108.3
N2—N3—C11	113.1 (5)	C9—C11—N3	106.3 (6)
N2—N3—C12	120.7 (5)	C9—C11—H111	127.7
C11—N3—C12	126.1 (5)	N3—C11—H111	126.0
C5—N4—C13	121.4 (5)	N3—C12—H121	109.3
C5—N4—C25	126.8 (5)	N3—C12—H122	109.1
C13—N4—C25	110.8 (5)	H121—C12—H122	110.4
C15—N5—C16	124.7 (5)	N3—C12—H123	109.2
C15—N5—H51	116.4	H121—C12—H123	107.0
C16—N5—H51	118.6	H122—C12—H123	111.8
F1—C1—C2	119.4 (6)	N4—C13—C14	102.8 (5)
F1—C1—C6	114.9 (6)	N4—C13—H131	110.2
C2—C1—C6	125.8 (6)	C14—C13—H131	112.0
C1—C2—N1	125.4 (6)	N4—C13—H132	110.9
C1—C2—C3	113.4 (5)	C14—C13—H132	112.7
N1—C2—C3	121.2 (5)	H131—C13—H132	108.1
C2—C3—C4	123.1 (5)	C13—C14—O2	103.4 (5)
C2—C3—H31	119.1	C13—C14—C15	113.5 (5)
C4—C3—H31	117.8	O2—C14—C15	109.3 (4)
C3—C4—C5	120.2 (5)	C13—C14—H141	111.0
C3—C4—H41	121.4	O2—C14—H141	110.2
C5—C4—H41	118.4	C15—C14—H141	109.4
N4—C5—C4	118.9 (6)	C14—C15—N5	112.6 (5)
N4—C5—C6	122.5 (5)	C14—C15—H151	109.3
C4—C5—C6	118.6 (5)	N5—C15—H151	107.6
C5—C6—C1	118.9 (6)	C14—C15—H152	109.0
C5—C6—H61	120.7	N5—C15—H152	108.1
C1—C6—H61	120.4	H151—C15—H152	110.1
N1—C7—C8	100.5 (5)	N5—C16—O3	123.2 (5)
N1—C7—H71	111.8	N5—C16—C17	114.3 (6)
C8—C7—H71	111.7	O3—C16—C17	122.4 (6)
N1—C7—H72	109.7	C16—C17—H171	110.9
C8—C7—H72	113.0	C16—C17—H172	109.7
H71—C7—H72	109.9	H171—C17—H172	108.3
C7—C8—N2	134.7 (6)	C16—C17—H173	108.9
C7—C8—C9	112.4 (5)	H171—C17—H173	108.4
N2—C8—C9	112.9 (6)	H172—C17—H173	110.6
C8—C9—C10	110.5 (5)	O2—C25—N4	110.2 (6)
C8—C9—C11	104.9 (5)	O2—C25—O1	121.1 (5)
C10—C9—C11	144.6 (6)	N4—C25—O1	128.6 (6)
C9—C10—N1	101.6 (5)