Development of Novel Bacterial Topoisomerase Inhibitors Assisted by Computational Screening

Abstract

Multidrug-resistant bacterial infections pose an ever-evolving threat to public health. Since the outset of the antibacterial age, bacteria have developed a multitude of diverse resistance mechanisms that suppress the effectiveness of current therapies. New drug entities, such as Novel Bacterial Topoisomerase Inhibitors (NBTIs), can circumvent this major issue. A computational docking model was employed to predict the binding to DNA gyrase of atypical NBTIs with novel pharmacophores. Synthesis of NBTIs based on computational docking and subsequent antibacterial evaluation against both Gram-positive and Gram-negative bacteria yielded congeners with outstanding anti-staphylococcal activity and varying activity against select Gram-negative pathogens.

Figure 1

Examples of a fluoroquinolone (ciprofloxacin) and NBTI (gepotidacin) are shown, with the key elements of the NBTI pharmacophore highlighted.

Figure 2

Assessing the predictive accuracy of docking results using binned classification: binning assessment of systems selected from benchmarking: (A) 6QTP, (B) 2XCS, and (C) 6FM4. For a series of known NBTIs, the predicted binding score was plotted versus the natural logarithm of the measured IC₅₀ value from a S. aureus DNA gyrase supercoiling assay. Agreement between experimental values and average Glide docking score was measured to determine the predictive accuracy of each DNA gyrase system (green: correct; yellow: within one bin; orange: within two; red: within three).

Figure 3

General structure of the targeted compounds.

Figure 4

Predicted docking poses and interactions with GyrA D83 in 2XCS of (A) monohydroxyl (7a) (1.6 Å to D83), (B) primary amine (9a) (1.8 Å to D83), and (C) anti-diol (22/23a) (1.6 and 1.9 Å to D83).

Figure 5

Overview of synthesized compounds.

Scheme 1. Synthesis of Ketones and Monohydroxyls, and Primary Amines

Reaction conditions: (i) NaO^tBu, Pd₂dba₃, (±)-BINAP, THF, 70 °C; (ii) HCl, MeOH; (iii) 1. AcOH, THF/MeOH, 4 Å MS. 2. NaCNBH₃; (iv) NaBH₄, MeOH; (v) 1. H₂NSOC(CH₃)₃, Ti(OEt)₄, THF, 70 °C. 2. NaBH₄, MeOH; (vi) HCl, MeOH.

Scheme 2. Synthesis of (E)-Olefins, Alkanes, and Syn-Diols

Reaction conditions: (i) 1. 5, AcOH, THF/MeOH, 4 Å MS. 2. NaCNBH₃; (ii) 4-CZIPN, Co(dmgH)(dmgH₂)Cl₂, HK₂PO₄, Et₃N, DMF, 440 nm light; (iii) H₂, 10% Pd/C, EtOH; (iv) AD-mix-α, ^tBuOH/water; (v) AD-mix-β, ^tBuOH/water.

Scheme 3. Synthesis of (Z)-Olefins and Anti-Diols

Reaction conditions: (i) KO^tBu, THF, 0 °C; (ii) HCl, MeOH; (iii) 1. 5, AcOH, THF/MeOH, 4 Å MS. 2. NaCNBH₃; (iv) AD-mix-α, ^tBuOH/water; (v) AD-mix-β, ^tBuOH/water.

Scheme 4. Synthesis of Alkane and Alkenes with Oxazinone RHS

Reaction conditions: (i) 4-CZIPN, Co(dmgH)(dmgH₂)Cl₂, HK₂PO₄, Et₃N, DMF, 440 nm light; (ii) HCl, MeOH; (iii) 1. 5, AcOH, THF/MeOH, 4 Å MS. 2. NaCNBH₃; (iv) H₂, 10% Pd/C, MeOH; (v) (Ir[dF(CF₃)ppy]₂(dtbpy))PF₆, ACN, 456 nm light; (vi) HCl, MeOH.

Scheme 5. Synthesis of Syn- and Anti-Diols with Oxazinone RHS

Reaction conditions: (i) AD-mix-α, ^tBuOH/water; (ii) AD-mix-β, ^tBuOH/water; (iii) AD-mix-α, ^tBuOH/water; (iv) AD-mix-β, ^tBuOH/water.

Scheme 6. Synthesis of Ketone, Monohydroxyl, and Monoamine with Oxazinone RHS

Reaction conditions: (i) NBS, ACN/water; (ii) K₂CO₃, MeOH; (iii) H₂, 10% Pd/C, EtOH; (iv) HCl, MeOH; (v) 1. 5, AcOH, THF/MeOH, 4 Å MS. 2. NaCNBH₃; (vi) DMP, DCM; (vii) HCl, MeOH; (viii) 1. H₂NSOC(CH₃)₃, Ti(OEt)₄, THF, 2. NaBH₄, MeOH; (ix) HCl, MeOH..

Scheme 7. Synthesis of Secondary Amine

Reaction conditions: (i) 1. 5, AcOH, THF/MeOH, 4 Å MS. 2. NaCNBH₃; (ii) HCl, MeOH; (iii) AcOH, THF/MeOH, 4 Å MS. 2. NaCNBH₃.

Figure 6

DNA cleavage assays with S. aureus DNA gyrase (left, A) and TopoIV (right, B).