Subnanomolar Inhibitor of Cytochrome bc₁ Complex Designed by Optimizing Interaction with Conformationally Flexible Residues

Abstract

Cytochrome bc1 complex (EC 1.10.2.2, bc1), an essential component of the cellular respiratory chain and the photosynthetic apparatus in photosynthetic bacteria, has been identified as a promising target for new drugs and agricultural fungicides. X-ray diffraction structures of the free bc1 complex and its complexes with various inhibitors revealed that the phenyl group of Phe274 in the binding pocket exhibited significant conformational flexibility upon different inhibitors binding to optimize respective π-π interactions, whereas the side chains of other hydrophobic residues showed conformational stability. Therefore, in the present study, a strategy of optimizing the π-π interaction with conformationally flexible residues was proposed to design and discover new bc1 inhibitors with a higher potency. Eight new compounds were designed and synthesized, among which compound 5c with a Ki value of 570 pM was identified as the most promising drug or fungicide candidate, significantly more potent than the commercially available bc1 inhibitors including azoxystrobin (AZ), kresoxim-methyl (KM), and pyraclostrobin (PY). To our knowledge, this is the first bc1 inhibitor discovered from structure-based design with a potency of subnanomolar Ki value. For all of the compounds synthesized and assayed, the calculated binding free energies correlated reasonably well with the binding free energies derived from the experimental Ki values with a correlation coefficient of r2 = 0.89. The further inhibitory kinetics studies revealed that compound 5c is a non-competitive inhibitor with respect to substrate cytochrome c, but is a competitive inhibitor with respect to substrate ubiquinol. Due to its subnanomolar Ki potency and slow dissociation rate constant (k−0 = 0.00358 s−1), compound 5c could be used as a specific probe for further elucidation of the mechanism of bc1 function and as a new lead compound for future drug discovery.

Molecular dynamics simulation exploration of unfolding and refolding of a ten-amino acid miniprotein

“…The bonds were constrained using the Shake method in all simulations. The simulation utilized particle mesh Ewald summation with a 12-Å cutoff for nonbonding interactions and an integration step of 2 fs (Pineda et al 2007;Saen-Oon et al 2008;Cramer and Truhlar 1999;Wu et al 2007;Huang et al 2008;Liu et al 2009;Zhao et al 2010;Yang et al 2011).…”

Electronic Connection Between the Quinone and CytochromecRedox Pools and Its Role in Regulation of Mitochondrial Electron Transport and Redox Signaling

“…For example, the synthetic inhibitor of the Q o site atovaquone is used in combination with other drugs to treat parasite diseases, in particular malaria, babesia, and toxoplasmosis (12,140,193). The potential use of cytochrome bc 1 inhibitors as drugs stimulates research to seek new compounds that would effectively target cells of protozoa parasites (15,127,278).…”

Design, Synthesis and Bioactivities of Novel Dichloro-Allyloxy-Phenol-Containing Pyrazole Oxime Derivatives

“…Pyrazole oximes are an important class of heterocyclic compounds which have drawn intense attention because of their good fungicidal [1,2], insecticidal [3][4][5], acaricidal [6], and anti-tobacco mosaic virus (TMV) activity [7]. For instance, Fenpyroximate (Figure 1), a potent agricultural acaricide with a vital pyrazole oxime backbone in the structure, possesses wonderful acaricidal property against some phytophagous mites such as Polyphagotarsonemus latus Banks and Tetranychus urticae Koch on different crops [8].…”