Central Linker Research Articles

Design, Synthesis, and Characterization of HBP-Vectorized Methotrexate Prodrug Molecule 1102-39: Evaluation of In Vitro Cytotoxicity Activity in Cell Culture Models, Preliminary In Vivo Safety and Efficacy Results in Rodents.

A novel bone-targeted prodrug, 1102-39, is discussed with the aim of enhancing the therapeutic effects of methotrexate (MTX) within bone tissues while minimizing systemic toxicity. Within the 1102-39 molecule, the central linker part forms a cleavable ester group, with MTX being also linked by a stable imine bond to the specially designed hydroxybisphosphonic (HBP) vector. Synthesized through a convergent approach starting from MTX, this prodrug advantageously modulates MTX's activity by selective esterification of its α-carboxyl group. In vitro tests revealed a 10-fold reduction in cytotoxicity compared to standard MTX, in alignment with prodrug behavior and correlated with gradual MTX release. In vivo in rodents, 1102-39 displayed preliminary encouraging antitumor effects on orthotopic osteosarcoma. Furthermore, various aspects of designing molecules for selective therapy in bone tissue based on bisphosphonate molecules as vectors for delivering active compounds to the bone are discussed. The 1102-39 molecule exhibits strong affinity for hydroxyapatite and a progressive release of MTX in aqueous environments, enhancing the safety and efficacy of bone-specific treatments and enabling sustained activity within bone and bone joints in the therapy of tumor and inflammation.

Functional investigation of a putative calcium-binding site involved in the inhibition of inositol 1,4,5-trisphosphate receptor activity.

A wide variety of factors influence inositol 1,4,5-trisphosphate (IP 3 ) receptor (IP 3 R) activity resulting in modulation of intracellular Ca 2+ release. This regulation is thought to define the spatio-temporal patterns of Ca 2+ signals necessary for the appropriate activation of downstream effectors. The binding of both IP 3 and Ca 2+ are obligatory for IP 3 R channel opening, however, Ca 2+ regulates IP 3 R activity in a biphasic manner. Mutational studies have revealed that Ca 2+ binding to a high-affinity pocket formed by the ARM3 domain and linker domain promotes IP 3 R channel opening without altering the Ca 2+ dependency for channel inactivation. These data suggest a distinct low-affinity Ca 2+ binding site is responsible for the reduction in IP 3 R activity at higher [Ca 2+ ]. We determined the consequences of mutating a cluster of acidic residues in the ARM2 and central linker domain reported to coordinate Ca 2+ in cryo-EM structures of the IP 3 R type 3. This site is termed the "CD Ca 2+ binding site" and is well-conserved in all IP 3 R sub-types. We show that the CD site Ca 2+ binding mutants where the negatively charged glutamic acid residues are mutated to alanine exhibited enhanced sensitivity to IP 3 -generating agonists. Ca 2+ binding mutants displayed spontaneous elemental Ca 2+ events (Ca 2+ puffs) and the number of IP 3 -induced Ca 2+ puffs was significantly augmented in cells stably expressing Ca 2+ binding site mutants. When measured with "on-nucleus" patch clamp, the inhibitory effect of high [Ca 2+ ] on single channel-open probability (P o ) was reduced in mutant channels and this effect was dependent on [ATP]. These results indicate that Ca 2+ binding to the putative CD Ca 2+ inhibitory site facilitates the reduction in IP 3 R channel activation when cytosolic [ATP] is reduced and suggest that at higher [ATP], additional Ca 2+ binding motifs may contribute to the biphasic regulation of IP 3 -induced Ca 2+ release.

Highly thermo- and photo-stable acceptor-acceptor′-acceptor type perylenediimide dimeric acceptors: Role of monofluorinating the central benzo[c][1,2,5]thiadiazole linking core

Acceptor-Acceptor′-Acceptor (A-A′-A) type perylene diimide (PDI)-based dimeric non-fullerene electron acceptors (NFEAs) have drawn the special attention but have not been sufficiently exploited. With that in mind, two A-A′-A type NFEAs, DTBT-(PDI-HD)2 and DTFBT-(PDI-HD)2, in which 4,7-di(thien-2-yl)benzo[c][1,2,5]thiadiazole (DTBT) and its monofluorinated 4,7-di(thien-2-yl)-5-fluorobenzo[c][1,2,5]thiadiazole (DTFBT) as central linkers, both N,N′-(2-hexyldecyl)-PDI (PDI-HD) units as flanked biwings, were successfully synthesized to probe into the influence of different electron-deficient linkers on thermo- and photo-stability, absorption, energy level, molecular configuration, exciton dissociation, charge mobility and solar cell performance. Both A-A′-A type acceptors with excellent thermal- and photo-stability possessed the complementary absorption ranging from 300 nm to 780 nm and matched ELUMO of −3.84 eV to −3.91 eV when pairing with PTB7-Th. Moreover, increased molecular dipole moment, slightly blue-shifted the maximum absorption peak, decreased the absorption coefficient and deepened the ELUMO were found after monofluorinating the benzothiadiazole. Conversely, the augmented aggregation both in solution and film effectively tuned the miscibility and morphology of active layer, contributing to the improvements of the exciton dissociation, charge mobility and photocurrent. Benefiting from this, monofluorinating the electron-deficient benzothiadiazole linker made the JSC increase from 3.72 to 7.19 mA cm−2, the FF enhance from 34.99 % to 38.18 % in DTFBT-(PDI-HD)2-based device when blending with PTB7-Th, contributing to 1.09 times increased PCE from 1.03 % to 2.15 % even in the adverse condition of 0.01 V dropped VOC. These results suggest that monofluorinating the electron-deficient benzothiadiazole linker is an effective approach for boosting the device efficiency via tuning the molecular aggregation and affecting the related morphology and charge mobility during the A-A′-A type PDI-based NFEAs.

Identifying Key Binding Interactions Between the Cardiac L-Type Calcium Channel and Calmodulin Using Molecular Dynamics Simulations.

Defects in the binding of the calcium sensing protein calmodulin (CaM) to the L-type calcium channel (CaV1.2) or to the ryanodine receptor type 2 (RyR2) can lead to dangerous cardiac arrhythmias with distinct phenotypes, such as long-QT syndrome (LQTS) and catecholaminergic ventricular tachycardia (CPVT). Certain CaM mutations lead to LQTS while other mutations lead to CPVT, but the mechanisms by which a specific mutation can lead to each disease phenotype are not well-understood. In this study, we use long, 2 μs molecular dynamics simulations and a multitrajectory approach to identify the key binding interactions between the IQ domain of CaV1.2 and CaM. Five key interactions are found between CaV1.2 and CaM in the C-lobe, 1 in the central linker, and 2 in the N-lobe. In addition, while 5 key interactions appear between residues 120-149 in the C-lobe of CaM when it interacts with CaV1.2, only 1 key interaction is found within this region of CaM when it interacts with the RyR2. We show that this difference in the distribution of key interactions correlates with the known distribution of CaM mutations that lead to LQTS or CPVT. This correlation suggests that a disruption of key binding interactions is a plausible mechanism that can lead to these two different disease phenotypes.

Investigation Into Novel Mukanadin B, Mukanadin D and Mukanadin F Derivatives as Antagonists of 5-HT1A Signalling.

Marine bromopyrrole alkaloids are a diverse family of natural products with a large array of biological applications. The mukanadin family is a group of molecules consisting of seven members (mukanadin A-G) that possess a range of biological activities. Inhibition of serotonergic signaling has been demonstrated by mukanadin B derivatives, presenting this chemical scaffold as a candidate for further SAR exploration. A library of thirteen novel mukanadin B and D derivatives with structural variation targeted at the pyrrole ring, central linker and hydantoin ring, were synthesized. These analogues were subsequently assessed for serotonergic antagonism, in addition to natural products, mukanadin B, D, F and 9-hydroxy mukanadin B. A collection of compounds exhibited significant 5-HT1A signaling, including five of the novel derivatives and two of the naturally occurring bromopyrroles, mukanadin B and F. Particular SAR information could be determined from these results, such as modification of the pyrrole ring being a well-tolerated strategy for improving serotonergic inhibition. Other changes to the pharmacophore led to significant reduction in activity such as saturation of the linker region, or no conclusive improvement in inhibitory activity such as a 9-OH group or replacement of the hydantoin ring with a triazole moiety.

A Modular and Catalytic Methodology To Access 2,5-Furan-Based Phenylene/Thiophene Oligomers through a One-Pot Decarboxylative Cross-Coupling from 5-Bromofurfural.

A library of 2,5-furan-based phenylene/thiophene oligomers were synthesized starting from 5-bromofurfural, a derivative of biomass-derived furfural. Varied electronic groups are coupled onto the furan motif, followed by the installation of a phenylene or thiophene central linker through a one-pot Pd-catalyzed decarboxylative cross-coupling reaction. Resulting oligomers containing the furan-phenylene-furan core possess high photoluminescent quantum yields in solution (83-98%), which are crucial for optoelectronic devices. Absorbance and photoluminescence maxima are tuned by changing peripheral functional groups and the center linker coupled onto the furan backbone.

Cyclization Reactions of 1,5-Diynes: Mechanisms and the Role of the Central Linker.

This study employed computational methods to elucidate the influence of structural features on the cyclization pathways of 1,5-diynes through the 5-endo-dig and 6-endo-dig mechanisms. The results revealed that the nature of the central linker played a significant role in dictating the preferred cyclization pathway. Notably, the capacity of this linker to extend delocalization appears to be the key factor governing the reaction pathway preference.

Biochemical and structural characterization of chlorhexidine as an ATP-assisted inhibitor against type 1 methionyl-tRNA synthetase from Gram-positive bacteria

Methionyl-tRNA synthetase (MetRS) catalyzes the attachment of l-methionine (l-Met) to tRNAMet to generate methionyl-tRNAMet, an essential substrate for protein translation within ribosome. Owing to its indispensable biological function and the structural discrepancies with human counterpart, bacterial MetRS is considered an ideal target for developing antibacterials. Herein, chlorhexidine (CHX) was identified as a potent binder of Staphylococcus aureus MetRS (SaMetRS) through an ATP-aided affinity screening. The co-crystal structure showed that CHX simultaneously occupies the enlarged l-Met pocket (EMP) and the auxiliary pocket (AP) of SaMetRS with its two chlorophenyl groups, while its central hexyl linker swings upwards to interact with some conserved hydrophobic residues. ATP adopts alternative conformations in the active site cavity, and forms ionic bonds and water-mediated hydrogen bonds with CHX. Consistent with this synergistic binding mode, ATP concentration-dependently enhanced the binding affinity of CHX to SaMetRS from 10.2 μM (no ATP) to 0.45 μM (1 mM ATP). While it selectively inhibited two representative type 1 MetRSs from S. aureus and Enterococcus faecalis, CHX did not show significant interactions with three tested type 2 MetRSs, including human cytoplasmic MetRS, in the enzyme inhibition and biophysical binding assays, probably due to the conformational differences between two types of MetRSs at their EMP and AP. Our findings on CHX may inspire the design of MetRS-directed antimicrobials in future.

Expression, purification, and biochemical analysis of the RNA-DNA hybrid helicase Sen1/SETX from Chaetomium thermophilum.

Yeast Sen1 and its vertebrate ortholog Senataxin (also known as SETX) are RNA-DNA resolving helicases. Sen1 and SETX are implicated in multiple critical nuclear functions not limited to but including DNA replication and repair, RNA processing, and transcription. These>200kDa helicases have a two-domain architecture with an N-terminal regulatory helical repeat array linked to an SF1b helicase motor core via a variable sized central linker of low complexity sequence. Given the size of these proteins, production of milligram quantities of protein that is suitable for biochemical, biophysical, and protein structural analysis has been challenging. To overcome these limitations, we developed a robust selectable high-yield YFP-fusion protein expression method for Sen1 production in mammalian cells, followed by purification on a high-affinity YFP-binding camelid nanobody support. Herein, we detail methods and protocols for the expression and purification of recombinant Sen1 from the thermophilic fungus Chaetomium thermophilum, and the quantitative characterization of its RNA-DNA duplex resolution activity.

Linker optimization and activity validation of a cell surface vimentin targeted homo-dimeric peptoid antagonist for lung cancer stem cells

Epithelial-to-mesenchymal transition (EMT) endows epithelia-derived cancer cells with properties of stem cells that govern cancer invasion and metastasis. Vimentin is one of the best studied EMT markers and recent reports indicate that vimentin interestingly translocated onto cell surface under various tumor conditions. We recently reported a cell surface vimentin (CSV) specific peptoid antagonist named JM3A. We now investigated the selective antagonist activity of the optimized homo-dimeric version of JM3A, JM3A-L2D on stem-like cancer cells or cancer stem cells (CSCs) over normal cells in non-small cell lung cancer (NSCLC). Homo-dimerization of JM3A provided the avidity effect and improved the biological activity compared to the monomeric version. We first optimized the central linker length of the dimer by designing seven JM3A derivatives with varying linker lengths/types and evaluated the anti-cancer activity using the standard MTS cell viability assay. The most optimized derivative contains a central lysine linker and two glycines, named JM3A-L2D, which displayed 100 nM vimentin binding affinity (Kd) with an anti-cancer activity (IC50) of 6.7 µM on H1299 NSCLC cells. This is a 190-fold improvement in binding over the original JM3A. JM3A-L2D exhibited better potency on high vimentin-expressing NSCLC cells (H1299 and H460) compared to low vimentin-expressing NSCLC cells (H2122). No activity was observed on normal bronchial HBEC3-KT cells. The anti-CSC activity of JM3A-L2D was evaluated using the standard colony formation assay and JM3A-L2D disrupted the colony formation with IC50 ∼ 400 nM. In addition, JM3A-L2D inhibited cell migration activity at IC50 ∼ 2 µM, assessed via wound healing assay. The underlying mechanism of action seems to be the induction of apoptosis by JM3A-L2D on high-vimentin expressing H1229 and H460 NSCLC cells. Our optimized highly CSV selective peptoid has the potential to be developed as an anti-cancer drug candidate, especially considering the high serum stability and economical synthesis of peptoids.

Isolable Bis‐BN‐Based Analogues of Müller's Hydrocarbon

Comprehensive SummaryMüller's hydrocarbon and its analogues are classical examples of Kekulé diradicaloids and have gained great attention. However, because of their high reactivities, their isolation and structural characterizations are still challenging. Herein, we report the isolation of two bis‐BN‐based analogues of Müller's hydrocarbon (1 and 2) as crystalline solids in moderate yields. Experimental results and theoretical studies demonstrated that compound 1 possessing the terminal 1,3,2‐diazaboryl groups is an open‐shell singlet diradicaloid, which is in contrast to the closed‐shell singlet ground states of the bis‐BN‐based analogues of Thiele's and Chichibabin's hydrocarbons with the same terminal groups, illustrating the strong influence of the central linkers on the ground state. Additionally, the replacement of the terminal 1,3,2‐diazaboryl groups in 1 with the bis(2,4,6‐triisopropylphenyl)boryl groups affords 2 with higher diradical character and a smaller singlet‐triplet energy gap.

Association of SARS-CoV-2 Nucleocapsid Protein Mutations with Patient Demographic and Clinical Characteristics during the Delta and Omicron Waves.

SARS-CoV-2 genomic mutations outside the spike protein that may increase transmissibility and disease severity have not been well characterized. This study identified mutations in the nucleocapsid protein and their possible association with patient characteristics. We analyzed 695 samples from patients with confirmed COVID-19 in Saudi Arabia between 1 April 2021, and 30 April 2022. Nucleocapsid protein mutations were identified through whole genome sequencing. 𝜒2 tests and t tests assessed associations between mutations and patient characteristics. Logistic regression estimated the risk of intensive care unit (ICU) admission or death. Of the 60 mutations identified, R203K was the most common, followed by G204R, P13L, E31del, R32del, and S33del. These mutations were associated with reduced risk of ICU admission. P13L, E31del, R32del, and S33del were also associated with reduced risk of death. By contrast, D63G, R203M, and D377Y were associated with increased risk of ICU admission. Most mutations were detected in the SR-rich region, which was associated with low risk of death. The C-tail and central linker regions were associated with increased risk of ICU admission, whereas the N-arm region was associated with reduced ICU admission risk. Consequently, mutations in the N protein must be observed, as they may exacerbate viral infection and disease severity. Additional research is needed to validate the mutations' associations with clinical outcomes.

The Nucleocapsid Proteins of SARS-CoV-2 and Its Close Relative Bat Coronavirus RaTG13 Are Capable of Inhibiting PKR- and RNase L-Mediated Antiviral Pathways.

Coronaviruses (CoVs), including severe acute respiratory syndrome CoV (SARS-CoV), Middle East respiratory syndrome CoV (MERS-CoV), and SARS-CoV-2, produce double-stranded RNA (dsRNA) that activates antiviral pathways such as PKR and OAS/RNase L. To successfully replicate in hosts, viruses must evade such antiviral pathways. Currently, the mechanism of how SARS-CoV-2 antagonizes dsRNA-activated antiviral pathways is unknown. In this study, we demonstrate that the SARS-CoV-2 nucleocapsid (N) protein, the most abundant viral structural protein, is capable of binding to dsRNA and phosphorylated PKR, inhibiting both the PKR and OAS/RNase L pathways. The N protein of the bat coronavirus (bat-CoV) RaTG13, the closest relative of SARS-CoV-2, has a similar ability to inhibit the human PKR and RNase L antiviral pathways. Via mutagenic analysis, we found that the C-terminal domain (CTD) of the N protein is sufficient for binding dsRNA and inhibiting RNase L activity. Interestingly, while the CTD is also sufficient for binding phosphorylated PKR, the inhibition of PKR antiviral activity requires not only the CTD but also the central linker region (LKR). Thus, our findings demonstrate that the SARS-CoV-2 N protein is capable of antagonizing the two critical antiviral pathways activated by viral dsRNA and that its inhibition of PKR activities requires more than dsRNA binding mediated by the CTD. IMPORTANCE The high transmissibility of SARS-CoV-2 is an important viral factor defining the coronavirus disease 2019 (COVID-19) pandemic. To transmit efficiently, SARS-CoV-2 must be capable of disarming the innate immune response of its host efficiently. Here, we describe that the nucleocapsid protein of SARS-CoV-2 is capable of inhibiting two critical innate antiviral pathways, PKR and OAS/RNase L. Moreover, the counterpart of the closest animal coronavirus relative of SARS-CoV-2, bat-CoV RaTG13, can also inhibit human PKR and OAS/RNase L antiviral activities. Thus, the importance of our discovery for understanding the COVID-19 pandemic is 2-fold. First, the ability of SARS-CoV-2 N to inhibit innate antiviral activity is likely a factor contributing to the transmissibility and pathogenicity of the virus. Second, the bat relative of SARS-CoV-2 has the capacity to inhibit human innate immunity, which thus likely contributed to the establishment of infection in humans. The findings described in this study are valuable for developing novel antivirals and vaccines.

Difluoroborate-based bichromophores: Symmetry relaxation and two-photon absorption

Given potential applications of multiphoton absorbers, in the present work we have studied the symmetry-relaxation effects in one- and two-photon absorption spectra in two bichromophore systems based on difluoroborate core linked by biphenylene or bianthracene moieties. We have employed a palette of experimental methods (synthesis, one- and two-photon spectroscopy, X-ray crystallography) and state-of-the-art computational methods to shed light on how symmetry relaxation, a result of twisting of building blocks, affects one- and two-photon absorption of the two studied fluorescent dyes. Electronic-structure calculations revealed that the planarity of central biphenyl moiety, as well as deviations from planarity up to 30–40 deg., ensure maximum values of two-photon transition strengths. Perpendicular arrangement of phenylene units in biphenylene moiety leads to 20% drop in the two-photon transition strengths. More detailed studies demonstrated that equilibrium structures of both compounds in chloroform solution show very different values of two-photon absorption cross sections at absorption band maxima, i.e. 224 GM for and 134 GM for biphenyle and bianthracene linkers, respectively. The latter value is in good agreement with experimental value obtained using Z-scan method. The difference in two-photon absorption cross section between both compounds can be rationalized based on equilibrium geometry differences, i.e. interplanar angle is 35 deg and 91 deg in the case of biphenylene and bianthracene moiety, respectively. It is thus not beneficial to introduce conformationally locked central linker based on bianthracene moiety.

Activation loop phosphorylation tunes conformational dynamics underlying Pyk2 tyrosine kinase activation

Pyk2 is a multidomain non-receptor tyrosine kinase that undergoes a multistage activation mechanism. Activation is instigated by conformational rearrangements relieving autoinhibitory FERM domain interactions. The kinase autophosphorylates a central linker residue to recruit Src kinase. Pyk2 and Src mutually phosphorylate activation loops to confer full activation. While the mechanisms of autoinhibition are established, the conformational dynamics associated with autophosphorylation and Src recruitment remain unclear. We employ hydrogen/deuterium exchange mass spectrometry and kinase activity profiling to map the conformational dynamics associated with substrate binding and Src-mediated activation loop phosphorylation. Nucleotide engagement stabilizes the autoinhibitory interface, while phosphorylation deprotects both FERM and kinase regulatory surfaces. Phosphorylation organizes active site motifs linking catalytic loop with activation segment. Dynamics of the activation segment anchor propagate to EF/G helices to prevent reversion of the autoinhibitory FERM interaction. We employ targeted mutagenesis to dissect how phosphorylation-induced conformational rearrangements elevate kinase activity above the basal autophosphorylation rate.

Molecular assembly with a figure-of-eight nanohoop as a strategy for the collection and stabilization of cyclo[18]carbon.

The recently synthesized novel figure-of-eight nanohoop with two strained oligoparaphenylenes (OPPs) was theoretically designed to collect and stabilize new allotropic carbon cyclo[18]carbon (C18) through molecular assembly. The size adaptability and shape complementarity of C18 to OPP make it possible for them to combine into extraordinary ring-in-ring supramolecules. Thermodynamic analysis of 2C18@OPP showed that the host-guest complex should spontaneously form below 404 K. Molecular dynamics (MD) simulations demonstrated that the assembly of C18 and OPP into host-guest complexes of up to 1 : 2 can occur at ambient temperature. Various real-space function analyses revealed that the nature of the non-covalent interaction between C18 and OPP is the van der Waals (vdW) attraction characterized by π-π stacking. Photoexcitation makes the host-guest complexes less stable in their S1 state by causing the central linker to flatten.

Recent advances in dopamine D2 receptor ligands in the treatment of neuropsychiatric disorders.

Dopamine is a biologically active amine synthesized in the central and peripheral nervous system. This biogenic monoamine acts by activating five types of dopamine receptors (D1-5 Rs), which belong to the G protein-coupled receptor family. Antagonists and partial agonists of D2 Rs are used to treat schizophrenia, Parkinson's disease, depression, and anxiety. The typical pharmacophore with high D2 R affinity comprises four main areas, namely aromatic moiety, cyclic amine, central linker and aromatic/heteroaromatic lipophilic fragment. From the literature reviewed herein, we can conclude that 4-(2,3-dichlorophenyl), 4-(2-methoxyphenyl)-, 4-(benzo[b]thiophen-4-yl)-1-substituted piperazine, and 4-(6-fluorobenzo[d]isoxazol-3-yl)piperidine moieties are critical for high D2 R affinity. Four to six atoms chains are optimal for D2 R affinity with 4-butoxyl as the most pronounced one. The bicyclic aromatic/heteroaromatic systems are most frequently occurring as lipophilic appendages to retain high D2 R affinity. In this review, we provide a thorough overview of the therapeutic potential of D2 R modulators in the treatment of the aforementioned disorders. In addition, this review summarizes current knowledge about these diseases, with a focus on the dopaminergic pathway underlying these pathologies. Major attention is paid to the structure, function, and pharmacology of novel D2 R ligands, which have been developed in the last decade (2010-2021), and belong to the 1,4-disubstituted aromatic cyclic amine group. Due to the abundance of data, allosteric D2 R ligands and D2 R modulators from patents are not discussed in this review.

Optimization of a cell surface vimentin binding peptoid to extract antagonist effect on lung cancer cells

Targeting cytoskeletal proteins that are uniquely translocated to cancer cell surface may provide an alternative path for conventional drug discovery. Vimentin is such a cell surface–translocated cytoskeletal protein (CSV) found in non small cell lung cancer (NSCLC). We previously reported the identification of CSV-binding peptoid, named JM3A. While JM3A had no antagonist effect, here we used multiple strategies to optimize the binding of JM3A on CSV and extract the antagonistic effect. We first performed minimum pharmacophore identification studies using alanine/sarcosine scans. These studies revealed that residues 1–4 and 8 (from the C-terminus) are not important and those residues 5–7 are important for JM3A binding to CSV. We then found that our previous N-terminal benzophenone (BP)-coupled JM3A (JM3A-BP), which was used for pull-down and target identification studies, displayed 3-fold binding enhancement. The molecular docking studies indicated that the BP moiety binds to a new binding pocket on the vimentin coil 2 fragment, and further studies using 12 benzophenone-like moieties indicated that at least two phenyl groups are needed to occupy this new binding site. Interestingly, the binding was improved when non-important and bulky residues at the 4th and 8th positions were replaced with methyl groups (JM3A-4,8-BP). We next dimerized JM3A-4,8-BP to enhance the binding via the “avidity effect,” using a central lysine linker to develop JM3A-4,8-BPD1 (EC50 = 300 nM). This showed 27- and 63-fold-improvement in binding over JM3A-4,8-BP and JM3A monomers, respectively. JM3A4,8BPD1 also displayed binding comparable to vimentin antibody. Finally, we observed an antagonist effect on H1299 NSCLC cell proliferation and viability from this most improved dimeric JM3A-4,8BPD1, which was not shown by the monomeric versions.

Designing boron-cluster-centered zwitterionic Y-shaped clocked QCA molecules

Quantum-dot cellular automata (QCA) is a nanoscale, transistor-less device technology. A single molecule may provide an elementary QCA device known as a cell. Molecular redox centers function as quantum dots, and the configuration of mobile charge on the dots encodes device states useful for classical computing. Molecular QCA may support ultra-high device densities and THz-scale switching speeds at room temperature. An applied electric field may be used to clock molecular QCA, providing power gain to boost weakened signals, as well as quasi-adiabatic device operation for minimal power dissipation in QCA devices and circuits. A zwitterionic, Y-shaped, three-dot molecule may function as a field-clocked QCA cell. We focus on the design of a counterion built into the center of the cell. Ab initio computations demonstrate that choice of counterion determines the number of mobile charges for encoding the device state on the three quantum dots. We use or as the central counterionic linker for two different Y-shaped, three-dot QCA molecules. While both molecules support the desired device states, the number of trapped charges in the counterion determines the number of mobile holes on the molecular quantum dots. This, in turn, determines whether the device state is encoded by a hole or an electron. This choice of encoding determines how the molecular QCA cell responds to a clocking field. The two counterions studied here lead to two QCA molecules with opposite responses to the clock, similar to the complementary responses of PMOS and NMOS transistors to gated voltage control.

Genome Protection by DNA Polymerase θ.

DNA polymerase θ (Pol θ) is a DNA repair enzyme widely conserved in animals and plants. Pol θ uses short DNA sequence homologies to initiate repair of double-strand breaks by theta-mediated end joining. The DNA polymerase domain of Pol θ is at the C terminus and is connected to an N-terminal DNA helicase-like domain by a central linker. Pol θ is crucial for maintenance of damaged genomes during development, protects DNA against extensive deletions, and limits loss of heterozygosity. The cost of using Pol θ for genome protection is that a few nucleotides are usually deleted or added at the repair site. Inactivation of Pol θ often enhances the sensitivity of cells to DNA strand-breaking chemicals and radiation. Since some homologous recombination-defective cancers depend on Pol θ for growth, inhibitors of Pol θ may be useful in treating such tumors.