ABSTRACT
The BCL-2 family of proteins (including the prosurvival proteins BCL-2, BCL-XL, and MCL-1) is an important target for the development of novel anticancer therapeutics. Despite the challenges of targeting protein-protein interaction (PPI) interfaces with small molecules, a number of inhibitors (called BH3 mimetics) have entered the clinic and the BCL-2 inhibitor, ABT-199/venetoclax, is already proving transformative. For BCL-XL, new validated chemical series are desirable. Here, we outline the crystallography-guided development of a structurally distinct series of BCL-XL/BCL-2 inhibitors based on a benzoylurea scaffold, originally proposed as α-helix mimetics. We describe structure-guided exploration of a cryptic "p5" pocket identified in BCL-XL. This work yields novel inhibitors with submicromolar binding, with marked selectivity toward BCL-XL. Extension into the hydrophobic p2 pocket yielded the most potent inhibitor in the series, binding strongly to BCL-XL and BCL-2 (nanomolar-range half-maximal inhibitory concentration (IC50)) and displaying mechanism-based killing in cells engineered to depend on BCL-XL for survival.
Subject(s)
Antineoplastic Agents/chemistry , Proto-Oncogene Proteins c-bcl-2/antagonists & inhibitors , Urea/analogs & derivatives , bcl-X Protein/antagonists & inhibitors , Animals , Antineoplastic Agents/metabolism , Antineoplastic Agents/pharmacology , Binding Sites , Biphenyl Compounds/chemistry , Biphenyl Compounds/metabolism , Cell Line , Cell Survival/drug effects , Crystallography, X-Ray , Humans , Hydrophobic and Hydrophilic Interactions , Inhibitory Concentration 50 , Mice , Molecular Dynamics Simulation , Nitrophenols/chemistry , Nitrophenols/metabolism , Piperazines/chemistry , Piperazines/metabolism , Protein Binding , Proto-Oncogene Proteins c-bcl-2/genetics , Proto-Oncogene Proteins c-bcl-2/metabolism , Structure-Activity Relationship , Sulfonamides/chemistry , Sulfonamides/metabolism , Surface Plasmon Resonance , Urea/metabolism , Urea/pharmacology , bcl-X Protein/genetics , bcl-X Protein/metabolismABSTRACT
The prosurvival BCL-2 proteins are attractive yet challenging targets for medicinal chemists. Their involvement in the initiation and progression of many, if not all, tumors makes them prime targets for developing new anticancer therapies. We present our approach based on de novo structure-based drug design. Using known structural information from complexes engaging opposing members of the BCL-2 family of proteins, we designed peptidomimetic compounds using a benzoylurea scaffold to reproduce key interactions between these proteins. A library stemming from the initial de novo designed scaffold led to the discovery of ligands with low micromolar potency (KD = 4 µM) and selectivity for BCL-XL. These compounds bind in the canonical BH3 binding groove in a binding mode distinct from previously known BCL-2 inhibitors. The results of our study provide insight into the design of a new class of antagonists targeting a challenging class of protein-protein interactions.
Subject(s)
Urea/analogs & derivatives , bcl-X Protein/antagonists & inhibitors , Crystallography, X-Ray , Drug Design , Magnetic Resonance Spectroscopy , Molecular Mimicry , Molecular Structure , Spectrometry, Mass, Electrospray Ionization , Structure-Activity Relationship , Urea/chemical synthesis , Urea/pharmacology , bcl-X Protein/chemistryABSTRACT
Four new tris-substituted bismuth(III) sulfonates of general formula [Bi(O(3)SR)(3)] (R = phenyl 1, p-tolyl 2, 2,4,6-mesityl 3 and S-(+)-10-camphoryl 4) have been synthesised and characterised. Their synthesis by solvent-free (SF) and solvent-mediated (SM) methods has been explored and their activity against Helicobacter pylori has been investigated. The compounds 1-4 display a remarkable in vitro activity against three laboratory strains of H. pylori (B128, 26,695 and 251) with minimum inhibitory concentration (MIC) values as low as 0.049 µg mL(-1) for the strains B128 and 26,695, and 0.781 µg mL(-1) for the clinical isolate 251. This places most MIC values in the nano-molar region and demonstrates the strong influence of the sulfonate group on the bactericidal properties. The novel solid state structure [Bi(8)(O(3)SMes)(20)(SO(4))(2)(H(2)O)(6)]·(C(7)H(8))(7)5·(C(7)H(8))(7), derived from the SM reaction under reflux conditions, is presented and the incorporation of the two inorganic sulfate anions in the centre of the wheel-like bismuth sulfonate cluster explained.
Subject(s)
Anti-Bacterial Agents/chemistry , Bismuth/chemistry , Coordination Complexes/chemistry , Helicobacter pylori/drug effects , Sulfonic Acids/chemistry , Anti-Bacterial Agents/chemical synthesis , Anti-Bacterial Agents/toxicity , Coordination Complexes/chemical synthesis , Coordination Complexes/toxicity , Crystallography, X-Ray , Helicobacter Infections/microbiology , Helicobacter pylori/isolation & purification , Microbial Sensitivity Tests , Molecular ConformationABSTRACT
As part of an anti-psychotic drug discovery program, we report the crystal structure of the title compound, C(24)H(23)ClN(4)O. The mol-ecule has a tricyclic framework with a characteristic buckled V-shaped pyridobenzoxazepine unit, with the central seven-membered heterocycle in a boat configuration. The piperazine ring displays a chair conformation with the 2-phenyl-ethyl substituent assuming an equatorial orientation. There are two crystallographically independent, but virtually identical, mol-ecules in the asymmetric unit.
ABSTRACT
Ketopantoate reductase is an essential enzyme for pantothenate (vitamin B5) synthesis and a potential antibiotic target. Here we report the 15N and 1HN, 13C', 13C(alpha) and 13C(beta) chemical shift assignments of the 34 kDa ketopantoate reductase in its apo state.
