Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase α-aminoacrylate intermediate

NMR-assisted crystallography—the integrated application of solid-state NMR, X-ray crystallography, and first-principles computational chemistry—holds significant promise for mechanistic enzymology: by providing atomic-resolution characterization of stable intermediates in enzyme active sites, including hydrogen atom locations and tautomeric equilibria, NMR crystallography offers insight into both structure and chemical dynamics. Here, this integrated approach is used to characterize the tryptophan synthase α-aminoacrylate intermediate, a defining species for pyridoxal-5′-phosphate–dependent enzymes that catalyze β-elimination and replacement reactions. For this intermediate, NMR-assisted crystallography is able to identify the protonation states of the ionizable sites on the cofactor, substrate, and catalytic side chains as well as the location and orientation of crystallographic waters within the active site. Most notable is the water molecule immediately adjacent to the substrate β-carbon, which serves as a hydrogen bond donor to the ε-amino group of the acid–base catalytic residue βLys87. From this analysis, a detailed three-dimensional picture of structure and reactivity emerges, highlighting the fate of the L-serine hydroxyl leaving group and the reaction pathway back to the preceding transition state. Reaction of the α-aminoacrylate intermediate with benzimidazole, an isostere of the natural substrate indole, shows benzimidazole bound in the active site and poised for, but unable to initiate, the subsequent bond formation step. When modeled into the benzimidazole position, indole is positioned with C3 in contact with the α-aminoacrylate Cβ and aligned for nucleophilic attack. Here, the chemically detailed, three-dimensional structure from NMR-assisted crystallography is key to understanding why benzimidazole does not react, while indole does.

A Panoramic Review of Benzimidazole Derivatives and Their Potential Biological Activity

The therapeutic potential of the benzimidazole nucleus dates back to 1944, being and important heterocycle system due to its presence in a wide range of bioactive compounds such as antiviral, anticancer, antibacterial, and so on, where optimization of substituents in this class of pharmacophore has resulted in many drugs. Its extensive biological activity is due to its physicochemical properties like hydrogen bond donor-acceptor capability,  stacking interactions, coordination bonds with metals as ligands and hydrophobic interactions; properties that allow them to easily bind with a series of biomolecules, including enzymes and nucleic acids, causing a growing interest in these types of molecules. This review aims to present an overview to leading benzimidazole derivatives, as well as to show the importance of the nature and type of substituents at the N1, C2, and C5(6) positions, when they are biologically evaluated, which can lead to obtaining potent drug candidate with significant range of biological activities.

Hydrogen bond activated glycosylation under mild conditions

Herein, we report a new glycosylation system for the highly efficient and stereoselective formation of glycosidic bonds using glycosyl N-phenyl trifluoroacetimidate (PTFAI) donors and a charged thiourea hydrogen-bond-donor catalyst. The...

Oxygen Stable Electrochemical CO2 Capture and Concentration through Alcohol Additives

Current methods for CO2 capture and concentration (CCC) are energy intensive due to their reliance on thermal cycles, which are intrinsically Carnot limited in efficiency. In contrast, electrochemically driven CCC (eCCC) can operate at much higher theoretical efficiencies. However, most reported systems are sensitive to O2, precluding their practical use. In order to achieve O2 stable eCCC, we pursued the development of molecular redox carriers with reduction potentials positive of the O2/O2- redox couple. Prior efforts to chemically modify redox carriers to operate at milder potentials resulted in a loss in CO2 binding. To overcome these limitations, we used common alcohols additives to anodically shift the reduction potential of a quinone redox carrier, 2,3,5,6-tetrachloro-p-benzoquinone (TCQ), by up to 350 mV, conferring O2 stability. Intermolecular hydrogen-bonding interactions to the dianion and CO2-bound forms of TCQ were correlated to alcohol pKa to identify ethanol as the optimal additive, as it imparts beneficial changes to both the reduction potential and CO2 binding constant, the two key properties for eCCC redox carriers. We demonstrate a full cycle of eCCC in aerobic simulated flue gas using TCQ and ethanol, two commercially available compounds. Based on the system properties, an estimated minimum of 21 kJ/mol is required to concentrate CO2 from 10% to 100%, or twice as efficient as state-of-the-art thermal amine capture systems and other reported redox carrier-based systems. Furthermore, this approach of using hydrogen-bond donor additives is general and can be used to tailor the redox properties of other quinones/alcohol combinations for specific CO2 capture applications.

A Pragmatic Pharmacophore Informatics Strategy to Discover New Potent Inhibitors Against Pim-3

Pim-3 (proviral integration site moloney murine leukemia virus-3) is an oncogene which encodes proteins belonging to serine/threonine kinase family, and PIM subfamily. It is generally over expressed in epithelial and hematological tumors. It is known to involve in numerous cellular functions such as cell growth, differentiation, survival, tumorigenesis and apoptosis. It also plays a crucial role in regulation of signal transduction cascades. Therefore it emerged as a hopefultherapeutic target for cancer treatment. In current study, indole derivatives having potent inhibitory activity against Pim 3 were taken and pharmacophore based virtual screening was carried out. A five point pharmacophore hypothesis with one hydrogen bond acceptor, one hydrogen bond donor and three aromatic rings i.e., ADRRR was developed with acceptable R2and Q2 values of 0.913 and 0.748 respectively. It was employed as a query and screening was conducted against Asinex and Otava lead library databases to screen out potent drug like candidates. The obtained compounds were subjected to SP, XP docking using 3D model of pim-3 which was constructed through comparative homology modelling and finally binding free energies were calculated for top hits. The docking and binding free energy studies revealed that six hit molecules showed higher binding energy in comparison to the best active molecule. Finally, MD simulations of the top hit with highest binding energy was carried out which indicated that the obtained hit N1 formed a stable complex with pim-3. We believe that these combined protocols will be helpful and cooperative to discover and design more potent pim-3 inhibitors in near future.

Computational Simulation of HIV Protease Inhibitors to the Main Protease (Mpro) of SARS-CoV-2: Implications for COVID-19 Drugs Design

SARS-CoV-2 is highly homologous to SARS-CoV. To date, the main protease (Mpro) of SARS-CoV-2 is regarded as an important drug target for the treatment of Coronavirus Disease 2019 (COVID-19). Some experiments confirmed that several HIV protease inhibitors present the inhibitory effects on the replication of SARS-CoV-2 by inhibiting Mpro. However, the mechanism of action has still not been studied very clearly. In this work, the interaction mechanism of four HIV protease inhibitors Darunavir (DRV), Lopinavir (LPV), Nelfinavir (NFV), and Ritonavire (RTV) targeting SARS-CoV-2 Mpro was explored by applying docking, molecular dynamics (MD) simulations, and MM–GBSA methods using the broad-spectrum antiviral drug Ribavirin (RBV) as the negative and nonspecific control. Our results revealed that LPV, RTV, and NFV have higher binding affinities with Mpro, and they all interact with catalytic residues His41 and the other two key amino acids Met49 and Met165. Pharmacophore model analysis further revealed that the aromatic ring, hydrogen bond donor, and hydrophobic group are the essential infrastructure of Mpro inhibitors. Overall, this study applied computational simulation methods to study the interaction mechanism of HIV-1 protease inhibitors with SARS-CoV-2 Mpro, and the findings provide useful insights for the development of novel anti-SARS-CoV-2 agents for the treatment of COVID-19.

Sustainable Preparation of Nanoporous Carbons via Dry Ball Milling: Electrochemical Studies Using Nanocarbon Composite Electrodes and a Deep Eutectic Solvent as Electrolyte

The urgent need to reduce the consumption of fossil fuels drives the demand for renewable energy and has been attracting the interest of the scientific community to develop materials with improved energy storage properties. We propose a sustainable route to produce nanoporous carbon materials with a high−surface area from commercial graphite using a dry ball−milling procedure through a systematic study of the effects of dry ball−milling conditions on the properties of the modified carbons. The microstructure and morphology of the dry ball−milled graphite/carbon composites are characterized by BET (Brunauer–Emmett–Teller) analysis, SEM (scanning electron microscopy), ATR−FTIR (attenuated total reflectance–Fourier transform infrared spectroscopy) and Raman spectroscopy. As both the electrode and electrolyte play a significant role in any electrochemical energy storage device, the gravimetric capacitance was measured for ball−milled material/glassy carbon (GC) composite electrodes in contact with a deep eutectic solvent (DES) containing choline chloride and ethylene glycol as hydrogen bond donor (HBD) in a 1:2 molar ratio. Electrochemical stability was tracked by measuring charge/discharge curves. Carbons with different specific surface areas were tested and the relationship between the calculated capacitance and the surface treatment method was established. A five−fold increase in gravimetric capacitance, 25.27 F·g−1 (G40) against 5.45 F·g−1, was found for commercial graphene in contact with DES. Optimal milling time to achieve a higher surface area was also established.

Combined Pharmacophore and Grid-Independent Molecular Descriptors (GRIND) Analysis to Probe 3D Features of Inositol 1,4,5-Trisphosphate Receptor (IP3R) Inhibitors in Cancer

Inositol 1, 4, 5-trisphosphate receptor (IP3R)-mediated Ca2+ signaling plays a pivotal role in different cellular processes, including cell proliferation and cell death. Remodeling Ca2+ signals by targeting the downstream effectors is considered an important hallmark in cancer progression. Despite recent structural analyses, no binding hypothesis for antagonists within the IP3-binding core (IBC) has been proposed yet. Therefore, to elucidate the 3D structural features of IP3R modulators, we used combined pharmacoinformatic approaches, including ligand-based pharmacophore models and grid-independent molecular descriptor (GRIND)-based models. Our pharmacophore model illuminates the existence of two hydrogen-bond acceptors (2.62 Å and 4.79 Å) and two hydrogen-bond donors (5.56 Å and 7.68 Å), respectively, from a hydrophobic group within the chemical scaffold, which may enhance the liability (IC50) of a compound for IP3R inhibition. Moreover, our GRIND model (PLS: Q2 = 0.70 and R2 = 0.72) further strengthens the identified pharmacophore features of IP3R modulators by probing the presence of complementary hydrogen-bond donor and hydrogen-bond acceptor hotspots at a distance of 7.6–8.0 Å and 6.8–7.2 Å, respectively, from a hydrophobic hotspot at the virtual receptor site (VRS). The identified 3D structural features of IP3R modulators were used to screen (virtual screening) 735,735 compounds from the ChemBridge database, 265,242 compounds from the National Cancer Institute (NCI) database, and 885 natural compounds from the ZINC database. After the application of filters, four compounds from ChemBridge, one compound from ZINC, and three compounds from NCI were shortlisted as potential hits (antagonists) against IP3R. The identified hits could further assist in the design and optimization of lead structures for the targeting and remodeling of Ca2+ signals in cancer.