First Review of Equilibrium Landscape of Ingress/Egress Channels and Gating Residues of the Cytochrome P450 3A4

The review document and changes made to Equilibrium Landscape of Ingress/Egress Channels and Gating Residues of the Cytochrome P450 3A4

Compositions and methods for treating bone deficit conditions

Compounds containing two aromatic systems covalently linked through a linker containing one or more atoms, or “linker” defined as including a covalent bond per se so as to space the aromatic systems at a distance 1.5-15 å, are effective in treating conditions associated with bone deficits. The compounds can be administered to vertebrate subjects alone or in combination with additional agents that promote bone growth or that inhibit bone resorption. They can be screened for activity prior to administration by assessing their ability to effect the transcription of a reporter gene coupled to a promoter associated with a bone morphogenetic protein and/or their ability to stimulate calvarial growth in model animal systems.Board of Regents, University of Texas Syste

p450 APO in Membrane Trajectory 1

The Cytochrome P450 (CYP) enzymes metabolize a variety of drugs, which may potentially lead to toxicity or reduced efficacy when drugs are co-administered. These drug-drug interactions are often manifested by CYP3A4, the most prevalent of all CYP isozymes. We carried out multiple MD simulations employing CAVER to quantify the channels, and Hidden Markov Models (HMM) to characterize the behavior of the gating residues. We discuss channel properties, bottleneck residues with respect to their likelihood to deem the respective channel ingress or egress, gating residues regarding their open or closed states, and channel location relative to the membrane. Channels do not display coordinated motion and randomly transition between different conformations. Gateway residues also behave in a random fashion. Our findings shed light on the equilibrium behavior of the gating residues and channels in the apo state

Functional Prediction of Binding Pockets

Putative function for targets with no known ligands has typically been determined from liganded homologous proteins using sequence and structure comparisons. However, it is debatable what percentage of sequence identity implies similar function, whereas structural similarity is focused on global folds and could miss divergent structures and novel global folds. The present study describes an approach to classify a diverse set of proteins and predict their function. Descriptors corresponding to structural, physicochemical, and geometric properties of the ligand-binding cavities of a collection of 434 complexes (17 protein families) were calculated and analyzed by statistical methods. The best model using discriminant function analysis (DFA) consisted of 371 proteins (15 families) and had correct classification rates of 90% and cross-validation 86%. DFA with one protein and a random sample of the remaining proteins led to 100% correct prediction of putative protein function for 10 of the 15 protein families

Elucidating Substrate Promiscuity in the Human Cytochrome 3A4

The human cytochrome P450 enzymes (CYPs) are heme-protein monooxygenases, which catalyze oxidative reactions of a broad spectrum of substrates. Consequently, they play a critical role in the metabolism of xenobiotics, such as drugs and carcinogens, and the catabolism of endogenous lipophilic factors. Bioavailability and toxicity, both of which can be related to CYPs, continue to pose problems in the development of new drugs. The isoform which metabolizes over one-third of drugs, CYP 3A4, was investigated employing ensemble-docking experiments of a 195-substrate library with induced fit and GOLD docking algorithms and a number of scoring functions. Enzyme conformations included three currently available CYP 3A4 crystal structures. All docking experiments were performed in duplicates with and without inclusion of crystallographic waters. Resultant poses were assessed based on accuracy of site of metabolism prediction. Analyses of the docked solutions pertaining to ranking efficacy, ligand molecular properties, stabilizing residues in the ligand–enzyme complexes, and metabolic reactions are discussed. Our analyses suggest that certain residues make favorable interactions with the bound substrates. Employing multiple receptor conformations enhances the accuracy of catalytic prediction, while ligand size and flexibility impact docking performance. The presence of waters observed in crystal complexes does not necessarily lead to improved performance

Elucidating Substrate Promiscuity in the Human Cytochrome 3A4

The human cytochrome P450 enzymes (CYPs) are heme-protein monooxygenases, which catalyze oxidative reactions of a broad spectrum of substrates. Consequently, they play a critical role in the metabolism of xenobiotics, such as drugs and carcinogens, and the catabolism of endogenous lipophilic factors. Bioavailability and toxicity, both of which can be related to CYPs, continue to pose problems in the development of new drugs. The isoform which metabolizes over one-third of drugs, CYP 3A4, was investigated employing ensemble-docking experiments of a 195-substrate library with induced fit and GOLD docking algorithms and a number of scoring functions. Enzyme conformations included three currently available CYP 3A4 crystal structures. All docking experiments were performed in duplicates with and without inclusion of crystallographic waters. Resultant poses were assessed based on accuracy of site of metabolism prediction. Analyses of the docked solutions pertaining to ranking efficacy, ligand molecular properties, stabilizing residues in the ligand–enzyme complexes, and metabolic reactions are discussed. Our analyses suggest that certain residues make favorable interactions with the bound substrates. Employing multiple receptor conformations enhances the accuracy of catalytic prediction, while ligand size and flexibility impact docking performance. The presence of waters observed in crystal complexes does not necessarily lead to improved performance

RSK1 vs. RSK2 Inhibitory Activity of the Marine β-Carboline Alkaloid Manzamine A: A Biochemical, Cervical Cancer Protein Expression, and Computational Study

Manzamines are complex polycyclic marine-derived β-carboline alkaloids with reported anticancer, immunostimulatory, anti-inflammatory, antibacterial, antiviral, antimalarial, neuritogenic, hyperlipidemia, and atherosclerosis suppression bioactivities, putatively associated with inhibition of glycogen synthase kinase-3, cyclin-dependent kinase 5, SIX1, and vacuolar ATPases. We hypothesized that additional, yet undiscovered molecular targets might be associated with Manzamine A’s (MZA) reported pharmacological properties. We report here, for the first time, that MZA selectively inhibited a 90 kDa ribosomal protein kinase S6 (RSK1) when screened against a panel of 30 protein kinases, while in vitro RSK kinase assays demonstrated a 10-fold selectivity in the potency of MZA against RSK1 versus RSK2. The effect of MZA on inhibiting cellular RSK1 and RSK2 protein expression was validated in SiHa and CaSki human cervical carcinoma cell lines. MZA’s differential binding and selectivity toward the two isoforms was also supported by computational docking experiments. Specifically, the RSK1-MZA (N- and C-termini) complexes appear to have stronger interactions and preferable energetics contrary to the RSK2–MZA ones. In addition, our computational strategy suggests that MZA binds to the N-terminal kinase domain of RSK1 rather than the C-terminal domain. RSK is a vertebrate family of cytosolic serine-threonine kinases that act downstream of the ras-ERK1/2 (extracellular-signal-regulated kinase 1/2) pathway, which phosphorylates substrates shown to regulate several cellular processes, including growth, survival, and proliferation. Consequently, our findings have led us to hypothesize that MZA and the currently known manzamine-type alkaloids isolated from several sponge genera may have novel pharmacological properties with unique molecular targets, and MZA provides a new tool for chemical-biology studies involving RSK1