Fragment-Based Exploration of Binding Site Flexibility in Mycobacterium tuberculosis BioA

Abstract

The PLP-dependent transaminase (BioA) of Mycobacterium tuberculosis and other pathogens that catalyzes the second step of biotin biosynthesis is a now well-validated target for antibacterial development. Fragment screening by differential scanning fluorimetry has been performed to discover new chemical scaffolds and promote optimization of existing inhibitors. Calorimetry confirms binding of six molecules with high ligand efficiency. Thermodynamic data identifies which molecules bind with the enthalpy driven stabilization preferred in compounds that represent attractive starting points for future optimization. Crystallographic characterization of complexes with these molecules reveals the dynamic nature of the BioA active site. Different side chain conformational states are stabilized in response to binding by different molecules. A detailed analysis of conformational diversity in available BioA structures is presented, resulting in the identification of two states that might be targeted with molecular scaffolds incorporating well-defined conformational attributes. This new structural data can be used as part of a scaffold hopping strategy to further optimize existing inhibitors or create new small molecules with improved therapeutic potential.

Disrupting the Constitutive, Homodimeric Protein–Protein Interface in CK2β Using a Biophysical Fragment-Based Approach

“…29 Subsequent SAR-by-catalog of fragment hits resulted in the crystallographic and thermodynamic characterization of a series of inhibitors. 29,30 This study has shown that thermally destabilizing fragments can be inhibitors and that caution should be applied before rejecting negatively shifting fragments for further evaluation. Furthermore, it has been suggested that thermally destabilizing fragments may have an additional value in promoting a more rapid degradation of the target protein.…”

“…To our knowledge, only one fragment-based study selected both thermally stabilizing and destabilizing fragments against homodimeric Mycobacterium tuberculosis BioA (an aminotransferase that uses a pyridoxal 5-phosphate cofactor) for follow-up studies, although no rationale was given for considering thermally destabilizing fragments. 29,30 Only one out of the 12 destabilizing fragments from the original screen against BioA produced a structure by cocrystallization. 29 Subsequent SAR-by-catalog of fragment hits resulted in the crystallographic and thermodynamic characterization of a series of inhibitors.…”

Structure-Based Optimization of Pyridoxal 5′-Phosphate-Dependent Transaminase Enzyme (BioA) Inhibitors that Target Biotin Biosynthesis in Mycobacterium tuberculosis

“…Several 3,4-bicyclic analogues ( 26–29 ) were inspired by the overlay of the acetylphenyl group of 6 or 12 with an inden-1-one moiety found and characterized in fragment screening (Figure 2B,C). 38 These compounds generally retained some biological activity, but only compound 26 with the identical inden-1-one of the original fragment hit improved upon the activity of 12 . A crystal structure of the complex with 26 (Table S1; PDB ID: 4XJO 36 ) was determined.…”

“…Both 6 and 12 derive some potency from planar stacking between the amide bond of the piperazinyl carbonyl and Tyr25. 38 The amide plane is absent in piperidinyl analogues, but in the complex with 39 , the ring pucker permits a perfectly positioned C–H on C4 of the piperidine to donate a H-bond to the Tyr25 π -system, whereas the position of the chlorophenyl ring is consistent with the positioning of the same moiety in the complex with 12 . To rationalize the complete lack of activity for 40 , the analogous crystal structure of 6 was examined.…”

Docking Studies for Various Antibacterial Benzilate Derivatives

“…Analysis of crystal structure of 4WYC revealed with hydrogen bonding interactions with nonpolar interaction like Trp398. The inhibitor is well associated with hydrophobic amino acids met61, Trp398, Trp64, Tyr407, and phe402 [10]. To validate the active site pocket the reference ligand was redocked and the docking score was found to be −6.032 kcal/mol.…”