The Difference a Single Atom Can Make: Synthesis and Design at the Chemistry-Biology Interface

Abstract

A Perspective of work in our laboratory on the examination of biologically active compounds, especially natural products, is presented. In the context of individual programs and along with a summary of our work, selected cases are presented that illustrate the impact single atom changes can have on the biological properties of the compounds. The examples were chosen to highlight single heavy atom changes that improve activity, rather than those that involve informative alterations that reduce or abolish activity. The examples were also chosen to illustrate that the impact of such single-atom changes can originate from steric, electronic, conformational, or H-bonding effects, from changes in functional reactivity, from fundamental intermolecular interactions with a biological target, from introduction of a new or altered functionalization site, or from features as simple as improvements in stability or physical properties. Nearly all the examples highlighted represent not only unusual instances of productive deep-seated natural product modifications and were introduced through total synthesis but are also remarkable in that they are derived from only a single heavy atom change in the structure.

Figure 1

Vancomycin binding to model ligands that contain single heavy atom exchanges.

Figure 2

Vancomycin analogues that incorporate single heavy atom changes in the binding pocket.

Figure 3

Vancomycin analogue that contains a single atom change in the binding pocket, reinstating activity against vancomycin-resistant bacteria, and two peripheral modifications that add two additional independent mechanisms of action.

Figure 4

Structure of [l-Dap²]ramoplanin A2 aglycon and a single heavy atom exchange in 49-membered macrocycle that substantially improves hydrolytic stability shown to limit the clinical use of ramoplanin.

Figure 5

10′-Fluorovinblastine and 10′-fluorovincristine, unique impact of an added single heavy atom substituent that improved target (tubulin) binding affinity and functional activity (30-fold).

Figure 6

Model of the 10′-fluoro binding site of 10′-fluorovinblastine (R = F, top) generated by adding the fluorine substituent to the X-ray structure of tubulin-bound vinblastine (R = H, bottom). Modeled complexes with larger substituents (R = Cl, Me, Br, I) exhibited increasingly larger destabilizing steric interactions as the substituent size progressively increased.

Figure 7

Active analogues required a single heavy atom exchange into the vinblastine structure (C20′ NH₂ for OH). In a plot of –log IC₅₀ (nM, HCT116) versus substituent σ_p, the analogues additionally displayed a predictable modulation of activity by a substituent (X) electronic effect, impacting benzamide carbonyl H-bonding with tubulin, some representing single heavy atom additions. All analogues shown are more active than vinblastine.

Figure 8

Plot of 20′ amide cLogP versus differential activity (IC₅₀ ratio) for isogenic HCT116 resistant (Pgp overexpression) and sensitive cell lines that progressively exchange in single heavy atoms or heteroatoms. The correlation defines a linear relationship between diminished resistance (ratio) that arises from reduced/abolished Pgp efflux, and a modulated physical property of the compounds (lipophilic character, cLogP) that can be predictably impacted by single atom changes. All compounds shown are more potent than vinblastine and display less resistance (vinblastine ratio = 88).

Figure 9

NMR structures of natural (+)- and ent-(−)-duocarmycin SA bound in the same AT-rich site of a deoxyoligonucleotide, illustrating the alkylation sites on complementary DNA stands offset by one base pair. Only the binding region of DNA is shown.

Figure 10

Single heavy atom exchange in the CC-1065 alkylation subunit that improves potency through a predicable reduction in intrinsic reactivity, placing it at an optimal point on a parabolic relationship between functional reactivity and activity.

Figure 11

Additional simplifying structural modifications, an example of removal of a single heavy atom (Me group) that improves potency by making the underlying DNA alkylation reaction sterically more accessible, and a recent efficacious prodrug design on a simplified structure.

Figure 12

Structure of bleomycin A2, NMR structure of bleomycin bound to a DNA cleavage site (full deoxyoligonucleotide and bleomycin disaccharide removed for clarity), key H-bonding role the pyrimidine C4 amine plays in guanine recognition, and role the minor groove guanine C2 amine plays in the recognition of bleomycin.

Figure 13

C2 and C4 methyl groups of the valerate linker in bleomycin induce a rigid, compact versus extended conformation productive for DNA cleavage; see Figure 12. Each heavy atom substituent independently increases the efficiency of DNA cleavage without impacting metal chelation, O₂ activation, or the cleavage reaction and without making direct contact with the target.

Figure 14

FAAH inhibitors.

Figure 15

Representative OL-135 analogues containing iterative single heavy atom changes or exchanges in the activating heterocycle. Reduction in the steric size of the heterocycle position 4 heavy atom (potency: N > O > CH) contributes to increased inhibitor potency.

Figure 16

–log K_i (μM) for FAAH versus Hammett σ_p, defining and quantitating a linear correlation between enzyme inhibition and the electronic impact of oxazole substituents on intrinsic reactivity of the electrophilic carbonyl of an α-ketoheterocycle (ρ = 3.0), some arising from single heavy atom substitution.

Figure 17

Superimposition of the X-ray structures of OL-135 (green) and its isomer (blue) bound to FAAH that illustrates the compensating impact of exchanging the location of two complementary heteroatoms.