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The hepatitis C virus (HCV) genome encodes a long polyprotein, which is processed by host cell and viral proteases to the individual structural and non-structural (NS) proteins. HCV NS3/4A serine proteinase (NS3/4A) is a non-covalent heterodimer of the N-terminal, ∼180-residue portion of the 631-residue NS3 protein with the NS4A co-factor. NS3/4A cleaves the polyprotein sequence at four specific regions. NS3/4A is essential for viral replication and has been considered an attractive drug target. Using a novel multiplex cleavage assay and over 2,660 peptide sequences derived from the polyprotein and from introducing mutations into the known NS3/4A cleavage sites, we obtained the first detailed fingerprint of NS3/4A cleavage preferences. Our data identified structural requirements illuminating the importance of both the short-range (P1-P1') and long-range (P6-P5) interactions in defining the NS3/4A substrate cleavage specificity. A newly observed feature of NS3/4A was a high frequency of either Asp or Glu at both P5 and P6 positions in a subset of the most efficient NS3/4A substrates. In turn, aberrations of this negatively charged sequence such as an insertion of a positively charged or hydrophobic residue between the negatively charged residues resulted in inefficient substrates. Because NS5B misincorporates bases at a high rate, HCV constantly mutates as it replicates. Our analysis revealed that mutations do not interfere with polyprotein processing in over 5,000 HCV isolates indicating a pivotal role of NS3/4A proteolysis in the virus life cycle. Our multiplex assay technology in light of the growing appreciation of the role of proteolytic processes in human health and disease will likely have widespread applications in the proteolysis research field and provide new therapeutic opportunities.

Hepatitis C is a treatment-resistant disease affecting millions of people worldwide. The hepatitis C virus (HCV) genome is a single-stranded RNA molecule. After infection of the host cell, viral RNA is translated into a polyprotein that is cleaved by host and viral proteinases into functional, structural and non-structural, viral proteins. Cleavage of the polyprotein involves the viral NS3/4A proteinase, a proven drug target. HCV mutates as it replicates and, as a result, multiple emerging quasispecies become rapidly resistant to anti-virals, including NS3/4A inhibitors. To circumvent drug resistance and complement the existing anti-virals, NS3/4A inhibitors, which are additional and distinct from the FDA-approved telaprevir and boceprevir α-ketoamide inhibitors, are required. To test potential new avenues for inhibitor development, we have probed several distinct exosites of NS3/4A which are either outside of or partially overlapping with the active site groove of the proteinase. For this purpose, we employed virtual ligand screening using the 275,000 compound library of the Developmental Therapeutics Program (NCI/NIH) and the X-ray crystal structure of NS3/4A as a ligand source and a target, respectively. As a result, we identified several novel, previously uncharacterized, nanomolar range inhibitory scaffolds, which suppressed of the NS3/4A activity in vitro and replication of a sub-genomic HCV RNA replicon with a luciferase reporter in human hepatocarcinoma cells. The binding sites of these novel inhibitors do not significantly overlap with those of α-ketoamides. As a result, the most common resistant mutations, including V36M, R155K, A156T, D168A and V170A, did not considerably diminish the inhibitory potency of certain novel inhibitor scaffolds we identified. Overall, the further optimization of both the in silico strategy and software platform we developed and lead compounds we identified may lead to advances in novel anti-virals.

Retinoid X receptor α (RXRα) and its N-terminally truncated version tRXRα play important roles in tumorigenesis, while some RXRα ligands possess potent anticancer activities by targeting and modulating the tumorigenic effects of RXRα and tRXRα. Here we describe NSC-640358 (N-6), a thiazolyl-pyrazole derived compound, acts as a selective RXRα ligand to promote TNFα-mediated apoptosis of cancer cell. N-6 binds to RXRα and inhibits the transactivation of RXRα homodimer and RXRα/TR3 heterodimer. Using mutational analysis and computational study, we determine that Arg316 in RXRα, essential for 9-cis-retinoic acid binding and activating RXRα transactivation, is not required for antagonist effects of N-6, whereas Trp305 and Phe313 are crucial for N-6 binding to RXRα by forming extra π-π stacking interactions with N-6, indicating a distinct RXRα binding mode of N-6. N-6 inhibits TR3-stimulated transactivation of Gal4-DBD-RXRα-LBD by binding to the ligand binding pocket of RXRα-LBD, suggesting a strategy to regulate TR3 activity indirectly by using small molecules to target its interacting partner RXRα. For its physiological activities, we show that N-6 strongly inhibits tumor necrosis factor α (TNFα)-induced AKT activation and stimulates TNFα-mediated apoptosis in cancer cells in an RXRα/tRXRα dependent manner. The inhibition of TNFα-induced tRXRα/p85α complex formation by N-6 implies that N-6 targets tRXRα to inhibit TNFα-induced AKT activation and to induce cancer cell apoptosis. Together, our data illustrate a new RXRα ligand with a unique RXRα binding mode and the abilities to regulate TR3 activity indirectly and to induce TNFα-mediated cancer cell apoptosis by targeting RXRα/tRXRα.

Retinoid X receptor [alpha] (RXR[alpha]) and its N-terminally truncated version tRXR[alpha] play important roles in tumorigenesis, while some RXR[alpha] ligands possess potent anti-cancer activities by targeting and modulating the tumorigenic effects of RXR[alpha] and tRXR[alpha]. Here we describe NSC-640358 (N-6), a thiazolyl-pyrazole derived compound, acts as a selective RXR[alpha] ligand to promote TNF[alpha]-mediated apoptosis of cancer cell. N-6 binds to RXR[alpha] and inhibits the transactivation of RXR[alpha] homodimer and RXR[alpha]/TR3 heterodimer. Using mutational analysis and computational study, we determine that Arg316 in RXR[alpha], essential for 9-cis-retinoic acid binding and activating RXR[alpha] transactivation, is not required for antagonist effects of N-6, whereas Trp305 and Phe313 are crucial for N-6 binding to RXR[alpha] by forming extra π-π stacking interactions with N-6, indicating a distinct RXR[alpha] binding mode of N-6. N-6 inhibits TR3-stimulated transactivation of Gal4-DBD-RXR[alpha]-LBD by binding to the ligand binding pocket of RXR[alpha]-LBD, suggesting a strategy to regulate TR3 activity indirectly by using small molecules to target its interacting partner RXR[alpha]. For its physiological activities, we show that N-6 strongly inhibits tumor necrosis factor [alpha] (TNF[alpha])-induced AKT activation and stimulates TNF[alpha]-mediated apoptosis in cancer cells in an RXR[alpha]/tRXR[alpha] dependent manner. The inhibition of TNF[alpha]-induced tRXR[alpha]/p85[alpha] complex formation by N-6 implies that N-6 targets tRXR[alpha] to inhibit TNF[alpha]-induced AKT activation and to induce cancer cell apoptosis. Together, our data illustrate a new RXR[alpha] ligand with a unique RXR[alpha] binding mode and the abilities to regulate TR3 activity indirectly and to induce TNF[alpha]-mediated cancer cell apoptosis by targeting RXR[alpha]/tRXR[alpha].

Retinoid X receptor a （RXRα） and its N-terminally trun- cated version tRXRα play important roles in tumorige. nesis, while some RXRg ligands possess potent anti- cancer activities by targeting and modulating the tumorigenic effects of RXRo and tRXRa. Here we describe NSC-640358 （N-6）, a thiazolyl-pyrazole derived compound, acts as a selective RXRα ligand to promote TNFα-mediated apoptosis of cancer cell. N-6 binds to RXRa and inhibits the transactivation of RXRα homod- imer and RXRa/TR3 heterodimer. Using mutational analysis and computational study, we determine that Arg316 in RXRa, essential for 9-cis-retinoic acid binding and activating RXRg transactivation, is not required for antagonist effects of N-6, whereas Trp305 and Phe313 are crucial for N-6 binding to RXRα by forming extra w-w stacking interactions with N-6, indicating a distinct RXRα binding mode of N-6. N-6 inhibits TR3-stimulated transactivation of Gal4-DBD-RXRα-LBD by binding to the ligand binding pocket of RXRa-LBD, suggesting a strategy to regulate TR3 activity indirectly by using small molecules to target its interacting partner RXRα. For its physiological activities, we show that N-6 strongly inhibits tumor necrosis factor a （TNFα）-induced AKT activation and stimulates TNFa-mediated apoptosis in cancer cells in an RXRa/tRXRo dependent manner.The inhibition of TNFα-induced tRXRα/p85α complex formation by N-6 implies that N-6 targets tRXRa to inhibit TNFα-induced AKT activation and to induce cancer cell apoptosis. Together, our data illustrate a new RXRa ligand with a unique RXRα binding mode and the abilities to regulate TR3 activity indirectly and to induce TNFa-mediated cancer cell apoptosis by targeting RXRα/tRXRα.

Human influenza A viruses (IAVs) cause global pandemics and epidemics. These viruses evolve rapidly, making current treatment options ineffective. To identify novel modulators of IAV–host interactions, we re-analyzed our recent transcriptomics, metabolomics, proteomics, phosphoproteomics, and genomics/virtual ligand screening data. We identified 713 potential modulators targeting 199 cellular and two viral proteins. Anti-influenza activity for 48 of them has been reported previously, whereas the antiviral efficacy of the 665 remains unknown. Studying anti-influenza efficacy and immuno/neuro-modulating properties of these compounds and their combinations as well as potential viral and host resistance to them may lead to the discovery of novel modulators of IAV–host interactions, which might be more effective than the currently available anti-influenza therapeutics.

5-Aminolevulinate synthase (EC 2.3.1.37) is the first enzyme in the heme biosynthetic pathway. It catalyzes a condensation of glycine and succinyl-CoA to form aminolevulinic acid, CoA-SH and CO2. This is the rate limiting and major regulatory step of heme biosynthesis in mammals and some bacteria. Recent site-directed mutagenesis studies of 5-aminolevulinate synthase identified amino acid residues involved in catalysis, substrate or cofactor binding. Although the roles of specific amino acid residues have been elucidated, much less is known about the involvement of 5-aminolevulinate synthase polypeptide chain arrangement in its folding, structure and function. To assess the importance of continuity of the 5-aminolevulinate synthase polypeptide chain, either random or engineered circularly permuted variants have been constructed. The circular permutation disrupts the continuity of a protein polypeptide chain by placing N- and C-termini into new locations without altering the amino acid composition of the protein. cDNA sequence analysis of the created active circularly permuted variants has shown that 5-aminolevulinate synthase is able to tolerate disruption of its polypeptide chain by circular permutation without loss of its activity. The central part of the protein, containing the amino acids previously shown to be crucial for cofactor binding and catalysis, was found to be intolerant to disruption. Four of the active circularly permuted variants were purified to homogeniosity and biochemically characterized. This allowed identification of two functional elements, with roles in catalysis and glycine binding. The functional element is defined as a continuous stretch of polypeptide chain for which integrity is required to maintain appropriate enzymatic function. The effects of circular permutation on the structure of 5-aminolevulinate synthase were further assessed using denaturant-induced equilibrium unfolding studies. The thermodynamic stabilities suggested that circular permutation primarily affected the folding of individual subunits while formation of the dimer interface remained similar among variants. The change in subunit folding was translated into non-wild type topologies of active sites as confirmed by cofactor fluorescence quenching and homology modeling studies. The homology modeling analysis also suggested that the two functional elements identified are defined structural domains of 5-aminolevulinate synthase, connected by 0an unstructured loop. However, these domains cannot be considered as autonomous folding units because swapping them modifies both the stability and folding kinetics of the protein.

Zika virus (ZIKV) serine protease, indispensable for viral polyprotein processing and replication, is composed of the membrane-anchored NS2B polypeptide and the N-terminal domain of the NS3 polypeptide (NS3pro). The C-terminal domain of the NS3 polypeptide (NS3hel) is necessary for helicase activity and contains an ATP-binding site. We discovered that ZIKV NS2B-NS3pro binds single-stranded RNA with a K d of ~0.3 μM, suggesting a novel function. We tested various structural modifications of NS2B-NS3pro and observed that constructs stabilized in the recently discovered “super-open” conformation do not bind RNA. Likewise, stabilizing NS2B-NS3pro in the “closed” (proteolytically active) conformation using substrate inhibitors abolished RNA binding. We posit that RNA binding occurs when ZIKV NS2B-NS3pro adopts the “open” conformation, which we modeled using highly homologous dengue NS2B-NS3pro crystallized in the open conformation. We identified two positively charged fork-like structures present only in the open conformation of NS3pro. These forks are conserved across Flaviviridae family and could be aligned with the positively charged grove on NS3hel, providing a contiguous binding surface for the negative RNA strand exiting helicase. We propose a “reverse inchworm” model for a tightly intertwined NS2B-NS3 helicase-protease machinery, which suggests that NS2B-NS3pro cycles between open and super-open conformations to bind and release RNA enabling long-range NS3hel processivity. The transition to the closed conformation, likely induced by the substrate, enables the classical protease activity of NS2B-NS3pro.

Zika virus (ZIKV) serine protease, indispensable for viral polyprotein processing and replication, is composed of an NS2B polypeptide that associates with a proteolytic N terminal fragment of NS3 polypeptide (NS3pro) to form NS2B-NS3pro. The larger C-terminal fragment of NS3 polypeptide contains helicase activity. In the present study, we discovered that ZIKV NS2BNS3pro efficiently binds single-stranded (ss) RNA (Kd ~0.3 uM), suggesting that the protease may have a novel function. We tested an array of NS2B-NS3pro modifications and found that NS2B NS3pro constructs that adopt the recently discovered super-open conformation could not bind ssRNA. Likewise, stabilization of NS2B-NS3pro in the closed (proteolytically active) conformation by substrate-like inhibitors abolished ssRNA binding. Therefore, we suggest that ssRNA binding occurs when ZIKV protease adopts the open conformation, which could be modeled using dengue NS2B-NS3pro in the open conformation. ssRNA binding competes with ZIKV NS2B-NS3pro protease activity, likely by shifting the complex into the open conformation. Modeling of ZIKV NS3 helicase activity based on homologous crystal structures suggests that the open conformation of NS3pro domains provides a positively charged surface contiguous with the NS3 helicase domain. Such a positively charged surface is well poised to bind ssRNA, providing an explanation for the previously observed requirement of NS3pro for RNA processivity by viral helicase. Our structure-function analyses suggest that binding of ssRNA by the protease domain of NS3 is likely to be a universal feature of Flaviviridae, given the high level of homology between NS3 protease-helicase proteins in this family. Competing Interest Statement The authors have declared no competing interest.