Interactive design and synthesis of a novel antibacterial agent

Abstract

. Can. J. Chem. 72, 105 1 (1994). P-Lactam compounds act on penicillin-recognizing enzymes via acylation of the hydroxyl group of an active site serine. When the resulting acyl enzyme is kinetically stable, as in the case of a penicillin-binding protein (PBP), the biosynthesis of a bacterial cell wall is inhibited, and death of the organism results. The de novo design of an antibacterial agent targeted to a PBP might be possible if the three-dimensional structural requirements of the equilibrium (i.e.,fit) and catalytic (i.e. reactivity) steps of the aforementioned enzymatic process could be determined. For a model of the active site of a PBP from Streptomyces R61, the use of molecular mechanics calculations to treat "fit," and ab initio molecular orbital calculations to treat "reactivity," leads to the idea that the carboxyl group (GI) and the amide N-H (G2) of the antibiotic are hydrogen bonded to a lysine amino group and a valine carbonyl group in the enzyme-substrate complex. These two hydrogen bonds place the serine hydroxyl group on the convex face of the antibiotic, in position for attack on the p-lactam ring by a neutral reaction, catalyzed by water, that involves a direct proton transfer to the p-lactam nitrogen. Molecular orbital calculations of structure-reactivity relations associated with this mechanism suggest that C=N is bioisosteric to the p-lactam N-C(=O), comparable to a p-lactam in its reactivity with an alcohol, and that the product RO(C-N)H is formed essentially irreversibly (-AE > 10 kcaUmo1). Accordingly, structures containing a G1 and a G2 separated by a C=N, and positioned in different ways with respect to this functional group, have been synthesized computationally and examined for their ability to fit to the PBP model. This strategy identified a 2H-5,6-dihydro-l,4-thiazine substituted by hydroxyl and carboxyl groups as a target for chemical synthesis. However, exploratory experiments suggested that the C=N of this compound equilibrates with endocyclic and exocyclic enamine tautomers. This required that the C2 position be substituted, and that the hydroxyl group not be attached to the carbon atom adjacent to the C=N. These conditions are met in a 2,2-dimethyl-3-(2-hydroxypropy1)-1,4-thiazine, which also exhibits the necessary fit to the PBP model. Two epimers of this compound have been synthesized, from D-and L-serine. The compound derived from L-serine is not active. The compound derived from D-serine exhibits antibacterial activity, but is unstable, and binding studies with PBP's have not been performed. It is hoped that these studies can be canied out if modification of the lead structure leads to compounds with improved chemical stability. Toutefois, des essais prkliminaires ont suggCrC que le C=N de ce composC serait en Cquilibre avec les Cnamines endocycliques et exocycliques tautombres. Cette caractkristique nCcessite que la position C2 soit substituCe et que le groupe hydroxyle ne soit pas attach6 au carbone adjacent du C=N. On rencontre ces conditions dans une 2,2-dimCthy1-3-(2...

Ab initio molecular orbital calculations on the neutral hydrolysis and methanolysis of azetidinones, including catalysis by water. Relationship to the mechanism of action of β-lactam antibiotics

“…Answers to these questions are currently being sought (32,33). Regardless of the eventual conclusions of those studies, the principal results of the present work are the conclusions that penicillin complexes with its receptor in such a way as to allow the most favourable mechanism for acylation of the active site serine to be attained, and that this mechanism can consist of a one-step water-catalyzed cleavage of the p-lactam bond, with proton transfer to nitrogen.…”

Synthesis of the stereoisomers of a novel antibacterial agent and interpretation of their relative activities in terms of a theoretical model of the penicillin receptor

“…Coupling of the lithium salts of R-and S-7 with Rand S-3 yielded the four stereoisomers of 8, each of which was obtained in analytically pure form. The structures and rotations of the isomers of 8 are shown in Table 2, which includes the structures and rotations of the four stereoisomers of 1 prepared from 8 by deprotection with formic acid, cyclization in water, and purification by preparative HPLC (4). Each of the isomers of 1 is believed to be ca.…”

“…of 1. Sixteen initial orientations of GI (C02-) and G2 (O-H) of this structure with respect to the amino (N) and carbonyl (V) groups of 12 were minimized (3,4) to produce, as the lowest energy structure, the complex shown in Fig Ten conformations of the RWSS diastereomer and seven conformations of the RS/SR diastereomer of 1, corresponding to torsion about the C5-C6, C3-C7, C7-C8, and C8-0 bonds, were generated using the dihedral driver of M M P~ (85) (14), and the energies of these structures were minimized. Each of the 34 RR, SS, RS, and SR structures was then docked to 12, as described above, the energies of the docked structures were minimized, and the rms deviations from the four-centred relationship of Fig.…”

“…We have proposed (4) that the N = C bond of an imine is bioisosteric to the N -C bond of the p-lactam group, and comparable to a p-lactam in its bioreactivity towards a hydroxyl group. A compound intended to fit to, and react with, the peni-'~a n a d a Council Killam Research Fellow 199C1992. cillin receptor in the same manner as penicillin itself might, therefore, contain an imine group properly positioned with respect to a G1 and a G2.…”

“…A reconciliation of these structural requirements with the chemical properties of dihydrothiazines suggested compound 1 as an example of a designed antibacterial agent. As summarized in Scheme 1 (4), the synthesis of 1 was accomplished starting with the racemic alcohol 2, prepared by a literature route from ethyl 2-methylcyclopropanecarboxylate (5), and the chiral lactones 3, prepared by a literature route from D-and L-serine (6). The compound having stereostructure l a , derived from D-serine, is an antibacterial agent; the isomer l b is not active.…”