Molecular Basis of Bcl-XL-p53 Interaction: Insights from Molecular Dynamics Simulations

Bcl-XL, an antiapoptotic Bcl-2 family protein, plays a central role in the regulation of the apoptotic pathway. Heterodimerization of the antiapoptotic Bcl-2 family proteins with the proapoptotic family members such as Bad, Bak, Bim and Bid is a crucial step in the apoptotic regulation. In addition to these conventional binding partners, recent evidences reveal that the Bcl-2 family proteins also interact with noncanonical binding partners such as p53. Our previous NMR studies showed that Bcl-XL: BH3 peptide and Bcl-XL: SN15 peptide (a peptide derived from residues S15-N29 of p53) complex structures share similar modes of bindings. To further elucidate the molecular basis of the interactions, here we have employed molecular dynamics simulations coupled with MM/PBSA approach. Bcl-XL and other Bcl-2 family proteins have 4 hydrophobic pockets (p1–p4), which are occupied by four systematically spaced hydrophobic residues (h1–h4) of the proapoptotic Bad and Bak BH3 peptides. We observed that three conserved hydrophobic residues (F19, W23 and L26) of p53 (SN15) peptide anchor into three hydrophobic pockets (p2–p4) of Bcl-XL in a similar manner as BH3 peptide. Our results provide insights into the novel molecular recognition by Bcl-XL with p53

Urokinase Inhibitor Design Based on Pharmacophore Model Derived from Diverse Classes of Inhibitors

It is widely documented that the progression of cancer cell invasion and metastasis is hinged on the ability of tumor cells to produce and recruit proteolytic enzymes. Among the diverse proteolytic enzyme systems produced by human cancers

Targeting FK506 binding proteins to fight malarial and bacterial infections : current advances and future perspectives

There is an urgent need for the design and development of new and selective drugs for the treatment of malaria and bacterial infections as these pathogens are developing resistance to presently available therapies. Malaria is a life threatening disease in many countries and responsible for almost one million deaths annually. In particular, drug-resistant malarial parasites are hindering effective control of malaria and prompting to find novel druggable targets and develop compounds with mechanism of action different from the conventional drugs. In this quest, efforts were made to determine three-dimensional structures of Plasmodium falciparum and Plasmodium vivax FK506 binding proteins which bind the macrolides (FK506 and rapamycin) and also demonstrate peptidylprolyl cis-trans isomerase activity in a similar manner as human FKBP12. Previous studies revealed that the immunosuppressive drug FK506 exhibits potential anti-malarial activity by binding FK506 binding domains (FKBD). This review focuses on three different types of FK506 binding proteins/domains in pathogens, their structural characteristics and biological roles. Binding ability of these proteins with the macrolides has opened new possibilities to develop selective inhibitors for these novel targets to combat the life threatening infections

Ligand Binding Mode Prediction by Docking: Mdm2/Mdmx Inhibitors as a Case Study

The p53-binding domains of Mdm2 and Mdmx, two negative regulators of the tumor suppressor p53, are validated targets for cancer therapeutics, but correct binding poses of some proven inhibitors, particularly the nutlins, have been difficult to obtain with standard docking procedures. Virtual screening pipelines typically draw from a database of compounds represented with 1D or 2D structural information from which one or more 3D conformations must be generated. These conformations are then passed to a docking algorithm that searches for optimal binding poses on the target protein. This work tests alternative pipelines using several commonly used conformation generation programs (LigPrep, ConfGen, MacroModel, and Corina/Rotate) and docking programs (GOLD, Glide, MOE-dock, and AutoDock Vina) for their ability to reproduce known poses for a series of Mdmx and/or Mdm2 inhibitors, including several nutlins. Most combinations of these programs using default settings fail to find correct poses for the nutlins but succeed for all other compounds. Docking success for the nutlin class requires either computationally intensive conformational exploration or an “anchoring” procedure that incorporates knowledge of the orientation of the central imidazoline ring

Co-factor binding pocket analyses.

<p>Comparison of NADPH/NADH binding pocket residues of (A) template structure yeast methylglyoxal/isovaleraldehyde reductase Gre2 (4PVD; Cyan colour), DHK (homology model; magenta), FabG from <i>Listeria monocytogenes</i> (4JRO; yellow), FabG from <i>Vibrio cholera</i> (4I08; green), and (B) FabG4 from <i>Mycobacterium tuberculosis</i> (3V1U; orange), FabG from <i>Bacillus</i> sp. (4NBU; gray). Three hotspot residues (HR1 to HR3) which are crucial in differentiating NADPH/NADH binding are highlighted as sticks and NADPH/NADH shown as yellow sticks in both the panels. Superimposition approach utilized to overlay the structures on template structures for comparison purpose.</p

Electrostatics role in substrate binding.

<p>Stereo view of electrostatic surface of DHK withmolecular docking predicted binding modes of Compound 41 (yellow sticks) and Compound 83 (green sticks). Negatively charged residues in hydrophilic sub pockets are labelled accordingly. The NADPH molecule shown as cyan sticks.</p

Delineating Substrate Diversity of Disparate Short-Chain Dehydrogenase Reductase from <i>Debaryomyces hansenii</i>

<div><p>Short-chain dehydrogenase reductases (SDRs) have been utilized for catalyzing the reduction of many aromatic/aliphatic prochiral ketones to their respective alcohols. However, there is a paucity of data that elucidates their innate biological role and diverse substrate space. In this study, we executed an in-depth biochemical characterization and substrate space mapping (with 278 prochiral ketones) of an unannotated SDR (DHK) from <i>Debaryomyces hansenii</i> and compared it with structurally and functionally characterized SDR <i>Synechococcus elongatus</i>. PCC 7942 FabG to delineate its industrial significance. It was observed that DHK was significantly more efficient than FabG, reducing a diverse set of ketones albeit at higher conversion rates. Comparison of the FabG structure with a homology model of DHK and a docking of substrate to both structures revealed the presence of additional flexible loops near the substrate binding site of DHK. The comparative elasticity of the cofactor and substrate binding site of FabG and DHK was experimentally substantiated using differential scanning fluorimetry. It is postulated that the loop flexibility may account for the superior catalytic efficiency of DHK although the positioning of the catalytic triad is conserved.</p></div

Homology model of DHK.

<p><b>A.</b> The sequence alignment between DHK and Gre2 (4PVD) sequence which was utilized to build the homology model of DHK, <b>B.</b> Cartoon representation of template structure and <b>C</b>. DHK homology model. Co-factor NADPH represented as yellow sticks and catalytic triad highlighted with sticks in both structures.</p

Purification of DHK and FabG.

<p><b>A</b>. SDS-PAGE analysis of the purified DHK. Lane 1: Purified DHK through Ni-NTA, Lane 2: Puregene Broad range marker, Lane 3: Superdex S75 purified DHK. <b>B.</b> SDS-PAGE of purified FabG Lane1: Low range marker Lane 2,3,4: gel purified FabG.</p