X-Ray studies on the structure and interactions of analgetic fenamates

Abstract

Non-steroidal anti-inflammatory drugs (NSAIDs) encompass a broad spectrum of compounds with varying degrees of analgesic, anti-inflammatory, and antipyretic activity. In spite of the diversity in their chemical nature, their biological activity is believed to be mainly due to their ability to inhibit the biosynthesis of prostaglandins (PG). The first chapter of this thesis presents a brief survey of the commonly used NSAIDs, followed by a brief discussion on the chemistry and the biosynthetic pathway of prostaglandins and their role in fever, inflammation, and pain. Also discussed are the various classes of inhibitors of the PG synthetase system and the structure-activity relationships in them.

Inasmuch as these drugs are known to be enzyme inhibitors, a prerequisite for elucidating the molecular mechanism of their action is a thorough understanding of their molecular geometry, the non-covalent interactions they are likely to be involved in, and the geometric and the electronic consequences of these interactions. This is sought to be achieved in this laboratory through the X-ray analysis of the drug molecules and their crystalline complexes with other suitable molecules. This ongoing programme, which has been discussed in Chapter 2, has so far been concerned primarily with analgesic pyrazole derivatives.

The previous work on fenamates, which is the common name for mefenamic acid, meclofenamic acid, flufenamic acid, and niflumic acid, has been confined to the X-ray analysis of the individual free compounds. The fenamate molecules essentially consist of three planar groupings, namely, two six-membered aromatic rings interconnected by an imino group and an ortho carboxyl group attached to one of the rings. The substituents on the other ring differentiate one fenamate from the other. A striking feature common to all the fenamate crystal structures is the near coplanarity of the carboxyl group with the ring bearing it and the imino nitrogen atom. Another interesting feature invariably found in these structures is the internal N–H···O hydrogen bond between the imino nitrogen and the adjacent carboxyl oxygen.

Having delineated the structural features of free fenamates, the obvious next step was the preparation and the X-ray analysis of their complexes. A major part of the thesis is concerned with this step.

The structure determination of the monohydrate of a 1:1 complex between niflumic acid and ethanolamine is reported in the third chapter. The complex crystallizes in the triclinic space group P1. The invariant features of the fenamates found in the crystal structures of their free forms are found to be retained in the niflumate ions of this structure. The complexation between the ethanolamine and niflumate ions is achieved through ionic and hydrogen-bonded interactions involving the deprotonated carboxylate group in niflumic acid. The two carboxylate oxygens participate in a specific interaction with the amino and the hydroxyl groups of ethanolamine through two nearly parallel hydrogen bonds. The hetero nitrogen atom of the 2-aminopyridine-3-carboxylic acid moiety is also involved in a hydrogen bond with a water molecule. The water molecule in the structure takes part in three hydrogen bonds, acting as donor in two and as acceptor in the third.

The polar groups of the niflumate and the ethanolamine ions, as well as the water molecule, aggregate around an inversion centre, forming an infinite column along the a-axis, while the apolar moieties, i.e., the aromatic rings, surround them.

Two complexes of meclofenamic acid could be crystallized, one with choline and the other with ethanolamine. The fourth chapter gives an account of the analysis of the monohydrate of the 1:1 complex between meclofenamic acid and choline. The crystals of the complex are orthorhombic, space group Pna2. The asymmetric unit contains two sets of molecules having remarkably similar geometries. They are related to each other by a pseudo-inversion centre. Due to this pseudo-symmetry, the distribution of molecules in the unit cell is nearly centrosymmetric while the space group is not. Interestingly, the meclofenamate ions retain the invariant structural features referred to earlier. The complex is stabilized by ionic interactions between the positive trimethylamino group of the choline ions and the deprotonated carboxylate group of the meclofenamate ions, and hydrogen bonds involving the carboxyl oxygens, the hydroxyl groups of choline, and the water molecules. The structure contains an interesting feature in which two water hydrogens are disordered between two possible hydrogen-bonding arrangements. As in the case of ethanolamine–niflumate monohydrate, in this structure also, the hydrophilic groups aggregate across (pseudo) inversion centres to form polar columns, while the hydrophobic groups surround them.

The fifth chapter presents the crystal structure of the 1:1 complex between meclofenamic acid and ethanolamine. The complex crystallizes in space group P1 with two crystallographically independent molecules in the unit cell. The two meclofenamate ions have nearly identical dimensions. They are related to each other by a non-integral screw axis. The two ethanolamine ions are also related to each other, but by another non-crystallographic axis with different rotational and translational components. The two meclofenamate ions in this structure also retain the invariant features mentioned earlier. The molecules in the unit cell are held together by ionic interactions and an intricate network of hydrogen bonds. The hydrophilic groups in the structure again form infinite columns surrounded by hydrophobic groups.

As indicated earlier, the fenamate molecule is essentially made up of three reasonably rigid planar groups connected by single bonds. The conformational flexibility of the molecule arising from possible rotations about these bonds was explored by conformational energy calculations employing semi-empirical methods.

The details of these calculations and the results derived therefrom are discussed in the sixth chapter. The calculations were performed for the molecules in both the ionization states, i.e., the neutral and the deprotonated anionic forms. The results obtained indicate that their flexibility is restricted to a rather limited region of conformational space. The observed minimum regions largely correspond to a coplanar arrangement of the carboxyl group with the ring to which it is attached. This arrangement facilitates the formation of an internal hydrogen bond between the imino nitrogen and a carboxylate oxygen. The theoretical calculations are in complete accord with the results of the crystallographic studies and thus provide an energetic rationale for the experimental findings on the fenamate molecules.

The results of the work reported in the thesis are summarized and the main conclusions outlined in the final chapter. Half of the molecules in each of the crystal structures containing fenamates are related to the other half by a crystallographic or non-crystallographic inversion centre. The centrosymmetrically related molecules are, however, not superimposable and are, therefore, enantiomorphous in the solid state.

The most striking invariant features in all the structures are the rigid coplanar geometry of the six-membered ring carrying the carboxyl group, the carboxyl group and the imino nitrogen atom, and also the internal hydrogen bond connecting the imino and the carboxyl groups. Conformational calculations provide a theoretical rationale for the occurrence of these features. They are retained even when the molecules interact strongly with other molecules, as in the complexes. The second ring, however, has some conformational flexibility. In all the crystal structures, the fenamate molecules interact, among themselves or with other molecules, primarily through the carboxyl group. A striking common feature of the crystal structures is the segregation of hydrophilic and hydrophobic regions in them. The structural features and the interaction patterns of fenamates obtained from the crystal structures provide a basis for informed speculation on structure-activity relationships in fenamates.

The crystal structures of phenylbutazone and oxyphenbutazone, two important members of the pyrazolidinedione family of anti-inflammatory analgesics, have already been reported. Monophenylbutazone is another member of this family. During attempts to crystallize it from a commercially procured sample, a hydroxy derivative of the compound, which was present as an impurity in the sample, readily crystallized. The X-ray analysis of these crystals, space group P2/n, is discussed in Appendix I. The molecule is made up of a five-membered pyrazolidinedione ring which carries a phenyl ring on one of the hetero nitrogen atoms and a butyl group on the tetrahedral carbon atom C(4), which also has the hydroxyl group as the fourth substituent. The five-membered and the six-membered rings in the structure are nearly coplanar. The hetero nitrogen atom to which the phenyl group is attached is planar, unlike in phenylbutazone and oxyphenbutazone. The other hetero nitrogen in the five-membered ring is, however, pyramidal. The molecule participates in two specific interactions, each involving two parallel hydrogen bonds related by an inversion centre. The hydroxyl oxygen and the pyramidal nitrogen act as the donors in these hydrogen bonds, while the two carbonyl oxygens act as the acceptors.

Part of the work described in this thesis has already been reported in the following publications:

“Structural Studies of Analgesics and Their Interactions. X. A Hydrated 1:1 Complex Between Niflumic Acid and Ethanolamine, CHFNO·HO,” Acta Cryst. (1983) C39, p. 1398 (with M. Vijayan).

“Structure and Interactions of Anti-inflammatory Analgesics. Crystal Structure of a 1:1 Complex Between Meclofenamic Acid and Choline,” Acta Cryst. (1984) A40, C-74 (with M. Vijayan).