Nonactin, (I), is a naturally occurring optically inactive macrotetrolide antibiotic whose activity includes the ability to transport cations across biological and artificial membranes. New antibiotics are urgently needed to combat persistent, emerging and re-emerging infectious diseases, hospital-acquired resistance, and bioterrorism agents. Currently, there is a renaissance of drug discovery from natural products. Exploration of microbial diversity in underexplored environments offers renewed hope for the discovery of novel antibiotics, anticancer agents, and other drugs from nature. In a pilot effort to explore the Great Lakes as an untapped freshwater environment for microbial resources from which new chemical entities may be obtained as antibiotics, dozens of actinomycete isolates were obtained from Lake Michigan sediment samples and found to produce chemical extracts with antimicrobial activities. In particular, a Streptomyces
sp. isolate was found to produce a significant amount of what was proven later to be nonactin anhydride.
Nonactin has been isolated previously from numerous bacterial sources as an antibiotic and anticancer agent (Corbaz et al.
; Solov’eva, 1973
; Wallhaeusser et al.
). This macrotetrolide ionophore consists of the (+)(−)(+)(−)-ester linkage of the enantiomeric nonactic acid building blocks. However, the elucidation of the solid-state structure of nonactin has proven difficult. Dunitz (1964
) determined that impure crystals (described as ‘not highly purified’) of nonactin gave diffraction patterns with para
-orthorhombic symmetry. Dornberger-Schiff (1966
) noted that the structure may be of the type ‘order–disorder’. The orthorhombic unit-cell dimensions were determined by Dominguez et al.
) as a
= 47.6 Å, b
= 31.5 Å and c
= 5.70 Å, and Dobler (1972
) reported the room-temperature order–disorder structure of nonactin in this cell, but noted that the superposition structure corresponds to the orthorhombic space group Pbam
with a unit cell of a
. Although Dobler reported the atomic parameters, he commented that the large magnitude of the standard deviations on bond distances and angles did not allow for a detailed discussion of the molecular geometry of nonactin. Dobler observed diffuse streaks in the diffraction pattern of crystals of nonactin; we also recorded streaking in the diffraction pattern of our crystal.
Herein we report molecular parameters of nonactin established with high precision. Our low-temperature (100 K) structural investigation of a colorless unknown (subsequently proven to be nonactin) proceeded as follows. The initial indexing of the unit cell suggested a C
-centered orthorhombic lattice consistent with the reported dimensions (a
= 31.147 Å, b
= 47.166 Å, c
= 5.569 Å and V
= 8180.55 Å3
), which is frequently a sign of trouble. The program CELL_NOW
) was used to index the reflections and the crystal appeared to be single. A full sphere of data was collected. The program XPREP
) suggested the space group Cmma
, which is encountered in the Cambridge Structural Database (CSD; Allen, 2002
) only 36 times. Not surprisingly, the structure could not be solved in this space group and a monoclinic unit cell was selected instead. Systematic absences were consistent with the space groups P
and the E
statistics were indiscriminate as to the centrosymmetry. Although the structure was successfully solved in P
, the refinement stalled, with an R
factor of ~22%. Scrutiny of the data revealed many F
values much higher than the corresponding F
values, a likely indication of twinning. The program PLATON
) was then used to analyze the data, and indeed pseudomerohedral twinning was detected. The suggested transformation matrix (00
00) corresponds to interchange of the a
axes that have very similar lengths. The suggested twin law was incorporated into the instruction file with a TWIN/BASF combination for the program XL
) and the batch scale factor refined to indicate a 45.08 (11)% contribution of the minor twin component. The resulting refinement converged to an R
factor of 4.30%. Fig. 1 shows the relationship between the primitive monoclinic unit cell and the apparent incorrect C
-centered orthorhombic unit cell. The monoclinic unit cell can be converted into the C
-centered orthorhombic cell with a transformation matrix (101,
0). A recent related example of pseudomerohedral twinning of cyclopentadecanone was reported by Noe et al.
Relationship between the correct monoclinic unit cell under P2/n symmetry and the apparent C-centered orthorhombic unit cell. The unique twofold symmetry axis is perpendicular to the plane of the page.
Nonactin (Fig. 2) crystallizes in a centrosymmetric lattice of P2/n symmetry, with two symmetry-independent half-molecules in the asymmetric unit (four molecules in the unit cell, Z = 4). Each molecule occupies a crystallographic twofold axis. The two independent molecules have virtually identical conformations with an approximate S
4 symmetry. The twofold and pseudo-S
4 axes pass through the molecular center of mass and are perpendicular to the plane of the macrocycle. The molecules form stacks in the  direction. There is a solvent-accessible void in the center of the macrocycle with an approximate volume of 69 Å3 (PLATON). The dimensions of this molecular cavity can be described with the centroid–centroid distances between the tetrahydrofuran rings related by the twofold axes. These dimensions are 7.688 (2) × 7.544 (2) Å in the O1 molecule and 7.563 (3) × 7.593 (2) Å in the O1A molecule. These continuous voids form channels in the crystal along the b axis (Fig. 3).
Figure 2 (a) The molecular structure of nonactin, with displacement ellipsoids shown at the 40% probability level and all H atoms omitted. (b) Sideways view of the two molecules along the crystallographic a axis. All atoms are shown (more ...)
Figure 3 A packing diagram of nonactin, viewed along the b axis. The voids in the center of the macrocycle form continuous channels in the lattice. All atoms are shown with 40% probability ellipsoids, but the O-atom ellipsoids are drawn with octant shading. (more ...)
The conformation of ‘free’ nonactin was compared with that observed in the previously reported nonactin complexes with Na+
(Dobler & Phizackerley, 1974
(Kilbourn et al.
(Sakamaki et al.
(Vishwanath et al.
) and NH4
(Neupert-Laves & Dobler, 1976
) using a new subroutine WBOX developed specifically for this project in the program OLEX2
(Dolomanov et al.
) to compute the dimensions of the smallest parallelepiped superscribing each of the nonactin complexes (Fig. 4). The obtained dimensions (Table 1) clearly show that ‘free’ nonactin per se
is unfolded and relatively square-planar, but becomes globular when encapsulating a cation, a fact noted by others and now supported quantitatively. For example, the dimensions of the parallelepiped superscribing nonactin are ~9 × 17 × 17 Å, whereas those for the parallelepiped encompassing nonactin coordinated to a Ca2+
cation are ~12 × 14 × 14 Å. In the four metal cationic complexes of nonactin, the macrocycle coordinates to the metal with four carbonyl and four tetrahydrofuran O atoms in a distorted cubic arrangement. In the cases of the smaller Na+
cations (hard Lewis bases), the metal–oxygen distances to the carbonyl O atoms are shorter, whereas in the cases of the larger Cs+
cations (softer Lewis bases), the distances to the tetrahydrofuran O atoms are shorter. It is noteworthy that encapsulation of larger Cs+
cations produces more spheroidal and compact structures – the ‘encompassing’ box sizes for the corresponding complexes are smaller than those of the complexes involving Na+
(Table 1). This is likely due to the better fit between the sizes of the larger cations and the internal nonactin cavity. In the case of the ammonium salt, the four H atoms of the cation form hydrogen-bonding interactions with four tetrahydrofuran O atoms. Thus, the conformational changes of nonactin are, as expected, dependent on the size and nature of the encapsulated cation.
Figure 4 Illustration of the smallest parallelepiped containing free nonactin (left) and nonactin coordinating a Cs+ cation. The box on the right is noticeably more isometric. All atoms are shown with their van der Waals spheres (see Table 1 (more ...)
Symmetry and size of selected nonactin complexes
The elusive structure of anhydrous ‘free’ nonactin has finally been unambiguously established. Nonactin crystallizes in a pseudomerohedrally twinned primitive monoclinic cell with two twin components of similar sizes.