Structures of complete extracellular receptor assemblies mediated by IL-12 and IL-23.

Cell-surface receptor complexes mediated by pro-inflammatory interleukin (IL)-12 and IL-23, both validated therapeutic targets, are incompletely understood due to the lack of structural insights into their complete extracellular assemblies. Furthermore, there is a paucity of structural details describing the IL-12-receptor interaction interfaces, in contrast to IL-23-receptor complexes. Here we report structures of fully assembled mouse IL-12/human IL-23-receptor complexes comprising the complete extracellular segments of the cognate receptors determined by electron cryo-microscopy. The structures reveal key commonalities but also surprisingly diverse features. Most notably, whereas IL-12 and IL-23 both utilize a conspicuously presented aromatic residue on their α-subunit as a hotspot to interact with the N-terminal Ig domain of their high-affinity receptors, only IL-12 juxtaposes receptor domains proximal to the cell membrane. Collectively, our findings will help to complete our understanding of cytokine-mediated assemblies of tall cytokine receptors and will enable a cytokine-specific interrogation of IL-12/IL-23 signaling in physiology and disease.

Dissecting the conformational complexity and mechanism of a bacterial heme transporter.

Iron-bound cyclic tetrapyrroles (hemes) are redox-active cofactors in bioenergetic enzymes. However, the mechanisms of heme transport and insertion into respiratory chain complexes remain unclear. Here, we used cellular, biochemical, structural and computational methods to characterize the structure and function of the heterodimeric bacterial ABC transporter CydDC. We provide multi-level evidence that CydDC is a heme transporter required for functional maturation of cytochrome bd, a pharmaceutically relevant drug target. Our systematic single-particle cryogenic-electron microscopy approach combined with atomistic molecular dynamics simulations provides detailed insight into the conformational landscape of CydDC during substrate binding and occlusion. Our simulations reveal that heme binds laterally from the membrane space to the transmembrane region of CydDC, enabled by a highly asymmetrical inward-facing CydDC conformation. During the binding process, heme propionates interact with positively charged residues on the surface and later in the substrate-binding pocket of the transporter, causing the heme orientation to rotate 180°.

Cryo-EM structures of pentameric autoinducer-2 exporter from Escherichia coli reveal its transport mechanism.

Bacteria utilize small extracellular molecules to communicate in order to collectively coordinate their behaviors in response to the population density. Autoinducer-2 (AI-2), a universal molecule for both intra- and inter-species communication, is involved in the regulation of biofilm formation, virulence, motility, chemotaxis, and antibiotic resistance. While many studies have been devoted to understanding the biosynthesis and sensing of AI-2, very little information is available on its export. The protein TqsA from Escherichia coli, which belongs to the AI-2 exporter superfamily, has been shown to export AI-2. Here, we report the cryogenic electron microscopic structures of two AI-2 exporters (TqsA and YdiK) from E. coli at 3.35 Å and 2.80 Å resolutions, respectively. Our structures suggest that the AI-2 exporter exists as a homo-pentameric complex. In silico molecular docking and native mass spectrometry experiments were employed to demonstrate the interaction between AI-2 and TqsA, and the results highlight the functional importance of two helical hairpins in substrate binding. We propose that each monomer works as an independent functional unit utilizing an elevator-type transport mechanism.

The cryo-EM structure of the bd oxidase from M. tuberculosis reveals a unique structural framework and enables rational drug design to combat TB.

New drugs are urgently needed to combat the global TB epidemic. Targeting simultaneously multiple respiratory enzyme complexes of Mycobacterium tuberculosis is regarded as one of the most effective treatment options to shorten drug administration regimes, and reduce the opportunity for the emergence of drug resistance. During infection and proliferation, the cytochrome bd oxidase plays a crucial role for mycobacterial pathophysiology by maintaining aerobic respiration at limited oxygen concentrations. Here, we present the cryo-EM structure of the cytochrome bd oxidase from M. tuberculosis at 2.5 Å. In conjunction with atomistic molecular dynamics (MD) simulation studies we discovered a previously unknown MK-9-binding site, as well as a unique disulfide bond within the Q-loop domain that defines an inactive conformation of the canonical quinol oxidation site in Actinobacteria. Our detailed insights into the long-sought atomic framework of the cytochrome bd oxidase from M. tuberculosis will form the basis for the design of highly specific drugs to act on this enzyme.

Conformation space of a heterodimeric ABC exporter under turnover conditions.

Cryo-electron microscopy (cryo-EM) has the capacity to capture molecular machines in action1-3. ATP-binding cassette (ABC) exporters are highly dynamic membrane proteins that extrude a wide range of substances from the cytosol4-6 and thereby contribute to essential cellular processes, adaptive immunity and multidrug resistance7,8. Despite their importance, the coupling of nucleotide binding, hydrolysis and release to the conformational dynamics of these proteins remains poorly resolved, especially for heterodimeric and/or asymmetric ABC exporters that are abundant in humans. Here we present eight high-resolution cryo-EM structures that delineate the full functional cycle of an asymmetric ABC exporter in a lipid environment. Cryo-EM analysis under active turnover conditions reveals distinct inward-facing (IF) conformations-one of them with a bound peptide substrate-and previously undescribed asymmetric post-hydrolysis states with dimerized nucleotide-binding domains and a closed extracellular gate. By decreasing the rate of ATP hydrolysis, we could capture an outward-facing (OF) open conformation-an otherwise transient state vulnerable to substrate re-entry. The ATP-bound pre-hydrolysis and vanadate-trapped states are conformationally equivalent; both comprise co-existing OF conformations with open and closed extracellular gates. By contrast, the post-hydrolysis states from the turnover experiment exhibit asymmetric ATP and ADP occlusion after phosphate release from the canonical site and display a progressive separation of the nucleotide-binding domains and unlocking of the intracellular gate. Our findings reveal that phosphate release, not ATP hydrolysis, triggers the return of the exporter to the IF conformation. By mapping the conformational landscape during active turnover, aided by mutational and chemical modulation of kinetic rates to trap the key intermediates, we resolved fundamental steps of the substrate translocation cycle of asymmetric ABC transporters.

Dihydropyridines and multidrug resistance: previous attempts, present state, and future trends.

Multidrug resistance is defined as the resistance of a tumor cell to the cytotoxic action of divergent drugs used in chemotherapy. Dihydropyridines are a class of calcium channel antagonists that were discovered to have a multidrug resistance reversing effect and prompted investigations resulting in the synthesis of hundreds of new derivatives. Most of the investigators tried to achieve two goals: a decrease in Ca²(+) channel-blocking activity and an increase in the multidrug resistance reversing effect. Most of the synthesized compounds failed in the later stages of studies especially in clinical trials because of pharmacokinetic or pharmacodynamic limitations. Therefore, it will be necessary to include new methods, such as combinatorial synthesis, and, more importantly, to apply computational methods based on global structure-activity relationship models that consider all problems. Moreover, some compounds should be synthesized that are effective on several multidrug resistance targets.

Comparative QSAR studies on toxicity of phenol derivatives using quantum topological molecular similarity indices.

Quantitative structure activity relationship (QSAR) analyses using a novel type of electronic descriptors called quantum topological molecular similarity (QTMS) indices were operated to describe and compare the mechanisms of toxicity of phenols toward five different strains (i.e., Tetrahymena pyriformis, L1210 Leukemia, Pseudomonas putida, Raja japonica and Cucumis sativus). The appropriate QSAR models for the toxicity data were obtained separately employing partial least squares (PLS) regression combined with genetic algorithms (GA), as a variable selection method. The resulting QSAR models were used to identify molecular fragments of phenol derivatives whose electronic properties contribute significantly to the observed toxicities. Using this information, it was feasible to discriminate between the mechanisms of action of phenol toxicity to the studied strains. It was found that toxicities of phenols to all strains, except with L1210 Leukemia, are significantly affected by electronic features of the phenolic hydroxyl group (C-O-H). Meanwhile, the resulting models can describe the inductive and resonance effects of substituents on various toxicities.

Dihydropyridines: evaluation of their current and future pharmacological applications.

The 1,4-dihydropyridines (DHPs), a class of drugs, possess a wide variety of biological and pharmacological actions, have represented one of the most important groups of calcium-channel-modulating agents and have experienced widespread use in the treatment of cardiovascular disease. Moreover, it has been demonstrated that DHPs could prove to be highly important as multidrug-resistance-reversing agents in cancer chemotherapy. Recent reports suggest that this class also has other notable activities, particularly as antimycobacterial and anticonvulsant agents. Finally, it might be possible for the DHP motif to serve as a scaffold for other pharmacological applications.

Application of MOLMAP approach for QSAR modeling of various biological activities using substituent electronic descriptors.

When using quantum chemical descriptors in quantitative structure-activity relationship (QSAR) studies, there is always a challenge between accuracy of calculation and the complexity and time of computation. Very recently, we proposed the use of substituents electronic descriptors (SEDs) instead of the electronic properties of whole molecule as new and expedite source of electronic descriptors. For instance, SED parameters can be calculated with the highest degree of accuracy in very low computation time. In this article, we used SED parameters in QSAR modeling of six different biological data sets including (i) the dissociation constants for a set of substituted imidazolines, (ii) the pKa of imidazoles, (iii) inverse agonist activity of indoles, (iv) the influenza virus inhibition activities of benzimidazoles, (v) inhibition of alcohol dehydrogenase by amides, and (vi) the natriuretic activity of sulfonamide. For poly-substituted molecules, SED parameters produce a vector of electronic descriptors for each substituent, and thus a matrix of SED parameters is obtained for each molecule. Consequently, a three-dimensional (3D) array is obtained by staking the descriptor data matrices of molecules beside each others. In addition to simple unfolding of the SED parameters, molecular maps of atom-level properties (MOLMAP) approach, as a novel data analysis method, was also applied to transfer 3D array of SED into new two-dimensional parameters using Kohonen network, following by genetic algorithm-based partial least square (GA-PLS) to connect a quantitative relationship between the Kohonen scores and biological activity. Accurate QSAR models were obtained by both approaches. However, the superiority of three-way analysis of SED parameters based on MOLMAP approach with respect to simple unfolding was obtained.

Quantum topological QSAR models based on the MOLMAP approach.

Quantum topological molecular similarity produces a two-dimensional array of descriptors for each molecule while a three-dimensional array is obtained by placing the descriptor data matrices of a set of molecules beside each other. Here, we use the multiway data analysis method called molecular maps (MOLMAP) of atom-level properties in a new way. We transferred the three-dimensional array of quantum topological molecular similarity descriptors into new two-dimensional parameters using Kohonen networks, followed by partial least squares. Six different data sets were analyzed by the proposed procedure, which were previously analyzed (Eur. J. Med. Chem. 2006 41 862) by partial least squares applied to unfolded data. They include: (i) the pK(a) of imidazoles, (ii) the ability of a set of indole derivatives to displace [(3)H] flunitrazepam from binding to bovine cortical membranes, (iii) the inhibitory effect of a set of benzimidazoles on the influenza virus, (iv) the interaction of amides with liver alcohol dehydrogenase, (v) inhibition of carbonic anhydrase by sulfonamides and (vi) the toxicity of a set of chlorophenols. Overall, the results showed better statistical results compared with simple unfolding. Furthermore, variable important in projection plots confirmed previous findings about active centers and even in some cases showed more accurate results.

Synthesis, QSAR and calcium channel modulator activity of new hexahydroquinoline derivatives containing nitroimidazole.

The discovery that 1,4-dihydropyridine class of calcium channel antagonists inhibit Ca2+ influx represented a major therapeutic advance in the treatment of cardiovascular disease. In contrast to the effects of known calcium channel blockers of the Nifedipine-type, the so-called calcium channel agonists, such as Bay K8644 and CGP 28392, increase calcium influx by binding at the same receptor regions. Our goal was to discover a dual cardioselective Ca2+-channel agonist/vascular selective smooth muscle Ca2+ channel antagonist third-generation 1,4-dihydropyridine drug which would have a suitable therapeutic profile for treating congestive heart failure (CHF) patients. A series of unsymmetrical alkyl, cycloalkyl and aryl ester analogues of 2-methyl-4-(1-methyl)-5-nitro-2-imidazolyl-5-oxo-1,4,5,6,7, 8-hexahydroquinolin-3-arboxylate were synthesized using modified Hantzsch reaction. All compounds show calcium antagonist activity on guinea-pig ileum longitudinal smooth muscle and some of them show agonist effect activity on guinea-pig auricle. Effect of structural parameters on the Ca2+ channel agonist/antagonist was evaluated by quantitative structure-activity relationship analysis. These compounds could be considered as a synthon for developing a suitable drug for treating CHF patients.

Dihydropyridine derivatives to overcome atypical multidrug resistance: design, synthesis, QSAR studies, and evaluation of their cytotoxic and pharmacological activities.

Multidrug resistance (MDR) is defined as resistance of tumor cells to the cytotoxic action of multiple structurally dissimilar and functionally divergent drugs commonly used in chemotherapy. Until now, there is no evidence for the effect of 1,4-dihydropyridines (DHPs) on atypical MDR, although there are some indications about the effect of DHPs on p-glycoprotein-mediated MDR. However, it was reported that a DHP derivative (Dexniguldipine) inhibited human DNA topoisomerase I through a non-competitive mechanism. Therefore, some derivatives of DHP were synthesized and their effect in reversing atypical MDR was evaluated. The results showed that two compounds were the potent reversals of atypical MDR. In addition, the intrinsic cytotoxicity of compounds was determined on four different cell lines. Furthermore, their Ca2+ channel blocking activity was evaluated and showed a clear structure-activity relationship (SAR) trend according to the moieties in C-4 position which confirmed the importance of C-4 moiety on Ca2+ channel blocking.

QSAR studies on the anesthetic action of some polyhalogenated ethers.

There has been an on-going debate about the mode of action of general anesthetics and until now, many sites have been postulated as target site for action of these compounds. Here, some quantum chemical-based quantitative structure-activity relationship (QSAR) models were developed for a set of polyhalogenated ethers in order to investigate the aspects of their anesthetic action, which is not completely defined yet, although some hypotheses have been suggested. A data set including 25 polyhalogenated methyl ethyl ethers were selected, and different descriptors were calculated for each molecule using density functional theory calculations, and subsequently some multilinear QSAR models were built by using different sets of the calculated molecular descriptors. The result showed that polar (polarizability) and non-polar (log P) parameters have mixed role on the anesthetic activity i.e. models with high statistical quality were obtained in combination with these two parameters. Also a good model between anesthetic action and electrostatic potentials was obtained, which may imply the important role of electronic interactions in the anesthetic activity of the compounds. Finally, a four-parametric QSAR model containing log P, molecular polarizability, most positive charge and an electrostatic potential parameters was obtained, which indicated that the anesthetic action of the polyhaloganted ethers may be proceeded through lipophilic, steric and columbic interactions.

Accurate prediction of the blood-brain partitioning of a large set of solutes using ab initio calculations and genetic neural network modeling.

A genetic algorithm-based artificial neural network model has been developed for the accurate prediction of the blood-brain barrier partitioning (in logBB scale) of chemicals. A data set of 123 logBB (115 old molecules and 8 new molecules) of a diverse set of chemicals was chosen in this study. The optimum 3D geometry of the molecules was estimated by the ab initio calculations at the level of RHF/STO-3G, and consequently, different electronic descriptors were calculated for each molecule. Indeed, logP as a measure of hydrophobicity and different topological indices were also calculated. A three-layered artificial neural network with backpropagation of an error-learning algorithm was employed to process the nonlinear relationship between the calculated descriptors and logBB data. Genetic algorithm was used as a feature selection method to select the most relevant set of descriptors as the input of the network. Modeling of the logBB data by the only quantum descriptors produced a 5:4:1 ANN structure with RMS error of validation and crossvalidation equal to 0.224 and 0.227, respectively. Better nonlinear model (RMS(V) and RMS(CV) equals to 0.097 and 0.099, respectively) was obtained by the incorporation of the logP and the principal components of the topological indices to electronic descriptors. The ultimate performances of the models were obtained by the application of the models to predict the logBB of 23 molecules that did not have contribution in the steps of model development. The best model produced RMS error of prediction 0.140, and could predict about 98% of variances in the logBB data.