Identification of novel dimers and chemical profiling of acid amide alkaloids in Piper nigrum

Peppers (Piper nigrum L.) are distinguished by their pungent flavor and aroma. Piperine is a major acid-amide alkaloid with a piperidine ring that gives pepper its flavor and scent. In plant metabolomics research, the accessibility of the chemical standards is critical for scientific credibility. We isolated and identified 10 novel dimers of acid amide alkaloids (9-15 and 20-22), along with 12 known monomers (1-6) and dimers (7, 8, 16-19) from black pepper. Subsequently, we found the distribution of monomers and dimers of acid amide alkaloids in black and white peppers by twenty-two acid amide alkaloids which we obtained using the molecular networking technique and multivariate analysis to reveal the molecular relationships between the acid amide alkaloids in black and white peppers. Our research delved into the chemical diversity of acid amide alkaloids in black and white peppers, which could help inform future culinary and potential medicinal utilization of pepper.

Synergistic Ni-W Dimer Sites Induced Stable Compressive Strain for Boosting the Performance of Pt as Electrocatalyst for the Oxygen Reduction Reaction

Alloying Pt catalysts with transition metal elements is an effective pathway to enhance the performance of oxygen reduction reaction (ORR), but often accompanied with severe metal dissolution issue, resulting in poor stability of alloy catalysts. Here, instead of forming traditional alloy structure, we modify Pt surface with a novel Ni-W dimer structure by the atomic layer deposition (ALD) technique. The obtained NiW@PtC catalyst exhibits superior ORR performance both in liquid half-cell and practical fuel cell compared with initial Pt/C. It is discovered that strong synergistic Ni-W dimer structure arising from short atomic distance induced a stable compressive strain on the Pt surface, thus boosting Pt catalytic performance. This surface modification by synergistic dimer sites offers an effective strategy in tailoring Pt with excellent activity and stability, which provides a significant perspective in boosting the performance of commercial Pt catalyst modified with polymetallic atom sites.

Solution Dynamics of Covalent Open-[60]Fullerene Dimers

The translational diffusivity of covalent open-[60]fullerene dimers in an organic solvent was found to be well describable by a prolate ellipsoid model while a monomeric open-[60]fullerene behaves like a sphere model. The water association dynamics were examined for two open-[60]fullerene dimers, showing a higher water affinity for the sp3-linked dimer relative to sp2-linked dimer owing to an effective orbital-orbital overlap identified by π(fullerene)→σ*(H2O) interactions as suggested by theoretical calculations.

N-terminal domain truncation yielded a unique dimer of polysaccharide hydrolase with enhanced enzymatic activity, stability and calcium ion independence

Domain engineering, including domain truncation, fusion, or swapping, has become a common strategy to improve properties of enzymes, especially glycosyl hydrolases. However, there are few reports explaining the mechanism of increased activity from a protein structure perspective. Amy703 is an alkaline amylase with a unique N-terminal domain. Prior studies have shown that N-Amy, a mutant without an N-terminal domain, exhibits improved activity, stability, and calcium ion independence. In this study, we have used X-ray crystallography to determine the crystal structure of N-Amy and used AlphaFold2 to model the Amy703 structure, respectively. We further used size exclusion chromatography to show that Amy703 existed as a monomer, whereas N-Amy formed a unique dimer. It was found that the N-terminus of one monomer of N-Amy was inserted into the catalytic domain of its symmetrical subunit, resulting in the expansion of the catalytic pocket. This also significantly increased the pKa of the hydrogen donor Glu350, thereby enhancing substrate binding affinity and contributing to increased N-Amy activity. Meanwhile, two calcium ions were found to bind to N-Amy at different binding sites, which also contributed to the stability of protein. Therefore, this study provided new structural insights into the mechanisms of various glycosyl hydrolases.

Spin-valley polarization and tunneling magnetoresistance in monomer, dimer, and trimer magnetic silicene superlattices

Monomer, dimer and trimer semiconductor superlattices are an alternative for bandgap engineering due to the possibility of duplicate, triplicate and in general multiply the number of minibands and minigaps in a specific energy region. Here, we show that monomer, dimer and trimer magnetic silicene superlattices (MSSLs) can be the basis for tunable magnetoresistive devices due to the multiplication of the peaks of the tunneling magnetoresistance (TMR). In addition, these structures can serve as spin-valleytronic devices due to the formation of two well-defined spin-valley polarization states by adjusting appropriately the superlattice structural parameters. We obtain these conclusions by studying the spin-valley polarization and TMR of monomer, dimer and trimer MSSLs. The magnetic unit cell is structured .

3-Amide-β-carbolines block the cell cycle by targeting CDK2 and DNA in tumor cells potentially as anti-mitotic agents

β-Carboline alkaloids are natural and synthetic products with outstanding antitumor activity. C3 substituted and dimerized β-carbolines exert excellent antitumor activity. In the present research, 37 β-carboline derivatives were synthesized and characterized. Their cytotoxicity, cell cycle, apoptosis, and CDK2- and DNA-binding affinity were evaluated. β-Carboline monomer M3 and dimer D4 showed selective activity and higher cytotoxicity in tumor cells than in normal cells. Structure-activity relationships (SAR) indicated that the amide group at C3 enhanced the antitumor activity. M3 blocked the A549 (IC50 = 1.44 ± 1.10 μM) cell cycle in the S phase and inhibited A549 cell migration, while D4 blocked the HepG2 (IC50 = 2.84 ± 0.73 μM) cell cycle in the G0/G1 phase, both of which ultimately induced apoptosis. Furthermore, associations of M3 and D4 with CDK2 and DNA were proven by network pharmacology analysis, molecular docking, and western blotting. The expression level of CDK2 was downregulated in M3-treated A549 cells and D4-treated HepG2 cells. Moreover, M3 and D4 interact with DNA and CDK2 at sub-micromolar concentrations in endothermic interactions caused by entropy-driven adsorption processes, which means that the favorable entropy change (ΔS > 0) overcomes the unfavorable enthalpy change (ΔH > 0) and drives the spontaneous reaction (ΔG < 0). Overall, these results clarified the antitumor mechanisms of M3 and D4 through disrupting the cell cycle by binding DNA and CDK2, which demonstrated the potential of M3 and D4 as novel antiproliferative drugs targeting mitosis.

Identification and structural analysis of dimeric chicken complement component 3d and its binding with chicken complement receptor 2

Complement component 3d (C3d), the final cleavage product of complement component C3, interacts with CR2 and thus plays a crucial role in linking the innate and adaptive immune systems. Additionally, human C3d executes various functions in its dimeric form, which is more effective than its monomeric form. In this study, we aimed to explored whether chicken C3d (chC3d) exhibits similar characteristics, namely dimerization and binding of dimeric chC3d to chicken CR2 (chCR2). We investigated the interaction and co-localization of chC3d with itself using coimmunoprecipitation and confocal laser scanning microscopy, respectively. Then, dimeric chC3d was detected using native polyacrylamide gel electrophoresis and western blotting, and its equilibrium dissociation constant KD (827 nM) was determined using surface plasmon resonance. Finally, the interaction modes of dimeric chC3d were identified using molecular docking simulations, which revealed that dimeric chC3d could crosslink with chCR2 receptor. Overall, our findings will facilitate future explorations of the chicken complement system.

Thermal degradation of (2R, 3R)-dihydromyricetin in neutral aqueous solution at 100 ℃

In the field of thermal degradation of flavonoids, current studies mainly focused on flavonols. However, the thermal degradation of dihydroflavonols in aqueous solution has received limited attention compared to flavonols. The single C2-C3 bonds of dihydroflavonols, which differs from the C2-C3 double bond in flavonols, may cause different degradation mechanisms. Dihydromyricetin (DMY) is a typical dihydroflavonol with six hydroxyl groups, and possesses various health effects. We explored the thermal degradation of DMY in neutral aqueous solution (pH 7) at 100 ℃. Ultra-performance liquid chromatography combined with photodiode array and electrospray ionization quadrupole-time-of-flight tandem mass spectrometric detection (UPLC-PDA-ESI-QTOF-MS/MS) provided suitable platform for exploring DMY degradation pathways, and negative ion mode was applied. Thermal treatment led to a decline in DMY level with time, accompanied by the appearance of various degradation products of DMY. Degradation mechanisms of DMY included isomerization, oxidation, hydroxylation, dimerization and ring cleavage. The pyrogallol-type ring B of DMY might be initially oxidized into ortho-quinone, which could further attack another DMY to form dimers. In addition, hydroxylation is likely to occur at C-2, C-3 of DMY or DMY dimers, which then further yields ring-cleavage products via breakage of the O1-C2 bond, C2-C3 bond, or C3-C4 bond. The 3-hydroxy-5-(3,3,5,7-tetrahydroxy-4-oxochroman-2-yl) cyclohexa-3,5-diene-1, 2-dione (m/z 333.0244) and unknown compound m/z 435.0925 were annotated as key intermediates in DMY degradation. Four phenolic acids, including 3,4,5-trihydroxybenzoic acid (m/z 169.0136, RT 1.4 min), 2,4,6-trihydroxyphenylglyoxylic acid (m/z 197.0084, RT 1.7 min), 2-oxo-2-(2,4,6-trihydroxyphenyl) acetaldehyde (m/z 181.0132, RT 2.4 min), and 2,4,6-trihydroxybenzoic acid (m/z 169.0139, RT 2.5 min) were identified as the major end products of DMY degradation. In addition, 5-((3,5dihydroxyphenoxy) methyl)-3-hydroxycyclohexa-3,5-diene-1,2-dione (m/z 261.0399, RT 11.7 min) and unidentified compound with m/z 329.0507 (RT 1.0 min) were also suggested to be end products of DMY degradation. These results provide novel insights on DMY stability and degradation products. Moreover, the heat treatment of DMY aqueous solution was found to gradually reduce the antioxidant activities of DMY, and even destroy the beneficial effect of DMY on the gut microbiota composition.

NMR assignment and dynamics of the dimeric form of soluble C-terminal domain major ampullate spidroin 2 from Latrodectus hesperus

Spider dragline silk has attracted great interest due to its outstanding mechanical properties, which exceed those of man-made synthetic materials. Dragline silk, which is composed of at least major ampullate spider silk protein 1 and 2 (MaSp1 and MaSp2), contains a long repetitive domain flanked by N-terminal and C-terminal domains (NTD and CTD). Despite the small size of the CTD, this domain plays a crucial role as a molecular switch that regulates and directs spider silk self-assembly. In this study, we report the 1H, 13C, and 15N chemical shift assignments of the Latrodectus hesperus MaSp2 CTD in dimeric form at pH 7. Our solution NMR data demonstrated that this protein contains five helix regions connected by a flexible linker.

Structural stability of R-state conformation of carbonmonoxyl sickle and normal hemoglobin dimer

A mutation at the sixth residue, glutamic acid to valine, in beta chain of hemoglobin distorts the entire shape of hemoglobin into a sickle shape. The investigation of the binding mechanisms of different chains of hemoglobin under the mutated condition can give an understanding of the molecular distortion. In this work, we have studied the binding mechanism between two chains in the dimer structure of the R-state conformation of carbonmonoxyl sickle hemoglobin and is compared with that of normal hemoglobin by using molecular dynamics simulations. The binding strength between α-chain (PROA) and β-chain (PROB) in hemoglobin dimer has been analyzed by estimating hydrogen bonds, salt bridges, hydrophobic interactions and non-bonded interactions (electrostatics and van der Waals). The quantitative estimation of aforementioned interactions depicts that the structural stability of normal hemoglobin dimer is found to be greater than that of sickle one. The outcomes of such interactions are also supported by the estimated free energy between the chains in R-state conformation of the dimers. The difference of binding free energy, calculated by utilizing the umbrella sampling technique, is found to be ≈ (0.67 ± 0.06) kcal/mol.Communicated by Ramaswamy H. Sarma.

Novel Bis-Artemisinin-Phloroglucinol hybrid molecules with dual anticancer and immunomodulatory Activities: Synthesis and evaluation

Bis-(10-deoxydihydroartemisinin)-phloroglucinol (9), has been synthesized in a one-step reaction and has demonstrated strong inhibition to cancer cell proliferation and immunosuppressive activity. The structure modification of the compound reduced its cytotoxicity, and among the analogs, bis-(10-deoxydihydroartemisinin)-phloroglucinol phenyl decanoate (16) showed significant reduction of ear swelling in a mouse model for DNFB-induced delayed-type hypersensitivity without observable toxicity in a dose-dependent manner.

Head-to-head comparison of different classes of FAP radioligands designed to increase tumor residence time: monomer, dimer, albumin binders, and small molecules vs peptides

PURPOSE

Fibroblast activation protein-α (FAP)-targeting radioligands have recently demonstrated high diagnostic potential. However, their therapeutic value is impaired by the short tumor residence time. Several strategies have been tested to overcome this limitation, but a head-to-head comparison has never been done. With the aim to identify strengths and limitations of the suggested strategies, we compared the monomer FAPI-46 versus (a) its dimer (FAPI-46-F1D), (b) two albumin binders conjugates (FAPI-46-Ibu (ibuprofen) and FAPI-46-EB (Evans Blue)), and (c) cyclic peptide FAP-2286.

METHODS

177Lu-labeled ligands were evaluated in vitro in cell lines with low (HT-1080.hFAP) and high (HEK-293.hFAP) humanFAP expression. SPECT/CT imaging and biodistribution studies were conducted in HT-1080.hFAP and HEK-293.hFAP xenografts. The areas under the curve (AUC) of the tumor uptake and tumor-to-critical-organs ratios and the absorbed doses were estimated.

RESULTS

Radioligands showed IC50 in the picomolar range. Striking differences were observed in vivo regarding tumor uptake, residence, specificity, and total body distribution. All [177Lu]Lu-FAPI-46-based radioligands showed similar uptake between the two tumor models. [177Lu]Lu-FAP-2286 showed higher uptake in HEK-293.hFAP and the least background. The AUC of the tumor uptake and absorbed dose was higher for [177Lu]Lu-FAPI-46-F1D and the two albumin binder conjugates, [177Lu]Lu-FAPI-46-Ibu and [177Lu]Lu-FAPI-46-EB, in HT1080.hFAP xenografts and for [177Lu]Lu-FAPI-46-EB and [177Lu]Lu-FAP-2286 in HEK293.hFAP xenografts. The tumor-to-critical-organs AUC values and the absorbed doses were in favor of [177Lu]Lu-FAP-2286, but tumor-to-kidneys.

CONCLUSION

The study indicated dimerization and cyclic peptide structures as promising strategies for prolonging tumor residence time, sparing healthy tissues. Albumin binding strategy outcome depended on the albumin binding moiety. The peptide showed advantages in terms of tumor-to-background ratios, besides tumor-to-kidneys, but its tumor uptake was FAP expression-dependent.

On the inter-monomer electron transfer in cytochrome bc1

Cytochrome bc₁ is a structural and functional homodimer. The catalytically-relevant inter-monomer electron transfer has been implicated by a number of experiments, including those based on analyses of the cross-dimer mutated derivatives. As some of the original data on these derivatives have recently been questioned, we extend kinetic analysis of these mutants to confirm the enzymatic origin of the observed activities and their relevance in exploration of conditions that expose electron transfer between the monomers. While obtained data consistently implicate rapid inter-monomer electron equilibration in cytochrome bc₁, the mechanistic and physiological meaning of this equilibration is yet to be established.

Unique dimeric structure of the DUF2891 family protein CJ0554 from Campylobacter jejuni

Campylobacter jejuni is a pathogenic bacterium that causes enteritis and Guillain-Barre syndrome in humans. To identify a protein target for the development of a new therapeutic against C. jejuni infection, each gene product of C. jejuni must be functionally characterized. The cj0554 gene of C. jejuni encodes a DUF2891 family protein with unknown functions. To provide functional insights into CJ0554, we determined and analyzed the crystal structure of the CJ0554 protein. CJ0554 adopts an (α/α)₆-barrel structure, which consists of an inner α₆ ring and an outer α₆ ring. CJ0554 assembles into a dimer in a unique top-to-top orientation that is not observed in its structural homologs, N-acetylglucosamine 2-epimerase superfamily members. Dimer formation was verified by analyzing CJ0554 and its ortholog protein through gel-filtration chromatography. The top of the CJ0554 monomer barrel harbors a cavity, which is connected to that of the second subunit in the dimer structure, generating a larger intersubunit cavity. This elongated cavity accommodates extra nonproteinaceous electron density, presumably as a pseudosubstrate, and is lined with generally catalytically active histidine residues that are invariant in CJ0554 orthologs. Therefore, we propose that the cavity functions as the active site of CJ0554.

Quantum Phase Diagram of a Frustrated Spin-1/2 Ferro-Antiferromagnetic Normal Ladder

In this work, we consider a frustrated two-leg spin-1/2 ladder composed of Heisenberg ferromagnetic and antiferromagnetic spin-1/2 chains, and nearest spins from different legs interact via Heisenberg type rung exchange interactions that can be either ferromagnetic or antiferromagnetic in nature. The competing exchange interactions in the system lead to five different quantum phases like ferromagnetic, non-collinear ferrimagnetic (NCF), m - 1 / 4 ${m - 1/4}$ , antiferromagnetic and dimer phases. The  quantum phase diagram is constructed for the Heisenberg spin-1/2 model and the phases are characterized using the correlation functions which are calculated by the density matrix renormalization group method. We also analyze the  stability of m - 1 / 4 ${m - 1/4}$ phase and calculate the pitch angle θ ${\left( \theta \right)}$ in the NCF phase.

Preventive or promotive effects of PRNP polymorphic heterozygosity on the onset of prion disease

The polymorphic heterozygosity of PRNP at codon 129 or 219 prevents the onset of sporadic Creutzfeldt-Jakob disease (sCJD). We investigated the association between polymorphic genotypes at codon 129 or 219 and comprehensive prion disease onset using non-CJD as a reference. EK heterozygotes at codon 219, versus EE homozygotes, showed a preventive effect on the extensive prion diseases-sCJD, genetic CJD (gCJD) with V180I or M232R mutation, and Gerstmann-Straussler-Scheinker disease with P102L mutation. No preventive effect was observed for E200K-gCJD and dura-grafted CJD (dCJD) in 129 MV and 219 EK heterozygotes. It was suggested that unlike other prion diseases, E200K-gCJD may not benefit from the preventive effect of 219 EK heterozygosity because complementary electrostatic interactions between PrP molecules at K200 and E219 might make homodimer formation easier. Comparison of sCJD and dCJD indicates that 219 EK heterozygosity strongly inhibits de novo synthesis of PrP^Sc (initial PrP^Sc formation), but does not inhibit accelerated propagation of existing PrP^Sc.

Designing Dimeric Lanthanide(III)-Containing Ionic liquids

Herein, we report on the preparation of liquid dimeric lanthanide(III)-containing compounds. Starting from the design of dimeric solids, we demonstrate that by tuning of anion and cation structures we can lower the melting points below room temperature, whilst maintaining the dimeric structure. Magnetic measurements could establish the spin-spin interactions of the neighboring lanthanide(III) ions in the liquid state at low temperatures, and matched the interactions of the analogous crystalline solid compounds.

A dimer-monomer transition captured by the crystal structures of cyanobacterial apo flavodoxin

In cyanobacteria and algae (but not plants), flavodoxin (Fld) replaces ferredoxin (Fd) under stress conditions to transfer electrons from photosystem I (PSI) to ferredoxin-NADP⁺ reductase (FNR) during photosynthesis. Fld constitutes a small electron carrier noncovalently bound to flavin mononucleotide (FMN), and also an ideal model for revealing the protein/flavin-binding mechanism because of its relative simplicity compared to other flavoproteins. Here, we report two crystal structures of apo-Fld from Synechococcus sp. PCC 7942, one dimeric structure of 2.09 Å and one monomeric structure of 1.84 Å resolution. Analytical ultracentrifugation showed that in solution, apo-Fld exists both as monomers and dimers. Our dimer structure contains two ligand-binding pockets separated by a distance of 45 Å, much longer than the previous structures of FMN-bound dimers. These results suggested a potential dimer-monomer transition mechanism of cyanobacterial apo-Fld. We further propose that the dimer represents the "standby" state to stabilize itself, while the monomer constitutes the "ready" state to bind FMN. Furthermore, we generated a new docking model of cyanobacterial Fld-FNR complex based on the recently reported cryo-EM structures, and mapped the special interactions between Fld and FNR in detail.

Recombinant Insulin-Like Growth Factor 1 Dimers: Receptor Binding Affinities and Activation Abilities

Insulin-like growth factor 1 (IGF-1) and its IGF-1 receptor (IGF-1R) belong to an important biological system that is involved in the regulation of normal growth, but that has also been recognized as playing a role in cancer. IGF-1R antagonists could be interesting for the testing of their potential antiproliferative properties as an alternative to IGF-1R tyrosine-kinase inhibitors or anti-IGF-1R monoclonal antibodies. In this study, we were inspired by the successful development of insulin dimers capable of antagonizing insulin effects on the insulin receptor (IR) by simultaneous binding to two separated binding sites and by blocking structural rearrangement of the IR. We designed and produced in Escherichia coli three different IGF-1 dimers in which IGF-1 monomers are interlinked through their N- and C-termini, with linkers having 8, 15 or 25 amino acids. We found that the recombinant products were susceptible to the formation of misfolded or reduced variants, but that some of them were able to bind IGF-1R in low nanomolar affinities and all of them activate IGF-1R proportionally to their binding affinities. Overall, our work can be considered as a pilot study that, although it did not lead to the discovery of new IGF-1R antagonists, explored the possibility of recombinant production of IGF-1 dimers and led to the preparation of active compounds. This work could inspire further studies dealing, for example, with the preparation of IGF-1 conjugates with specific proteins for the study of the hormone and its receptor or for therapeutic applications.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s10989-023-10499-1.

Modelling the octanol-air partition coefficient of aromatic pollutants based on the solvation free energy and the dimer effect

In this study, generalized predictive models were developed to estimate K_OA of four kinds of aromatic pollutants based on the calculated solvation free energy and taking the dimer effect into account. Uncorrected log K_OA values, which were directly estimated from the calculated solvation free energy of individual molecules, underestimated experimental values, and the deviation increased with increasing log K_OA. Dimers were found to greatly affect the apparent K_OA values of these aromatic pollutants, which were driven by π-π interactions. London dispersion and exchange-repulsion terms were identified to be dominant components of the underlying π-π interactions. It is interesting to find that the π-π interactions of polybrominated diphenyl ethers correlate with not only the molecular polarizability but also the size of opposing aromatic surfaces, which leads to a different trend of π-π interactions from other aromatic pollutants. A universal quantitative structure-activity relationship model was developed to estimate the proportion of dimers based on five molecular structural descriptors relevant to the π-π interactions. After calibration with the dimer effect, estimations of log K_OA were consistent with experimental values. Therefore, the dimer effect should be taken into consideration when investigating the partition behavior of aromatic pollutants, and the solvation free energy model could be an alternative method for the prediction of K_OA.

Aggregation induced spectral splitting and Fermi resonance of Ethylene Carbonate in binary mixture

The vibration band of the ring stretching (ν₁₄), the fundamental ring breathing (ν₁₇) and the Fermi resonance band of carbonyl stretching mixing with the overtone of the ring breathing (ν_{5 +} 2ν₁₇) have been investigated in solid ethylene carbonate (EC) and EC/CH₃CN and EC/CHCl₃ binary mixture. Dimer structure with aggregation-induced spectral splitting model (AIS) was applied to calculate the vibration spectra using the B3LYP-D3/6-311+G (d,p) procedure. The noncoincidence effect (NCE) and concentration induced frequency shifts of the ν₁₄ and ν₅ could be well explained by AIS model based on the dimer structure. Four bands were observed with two in the isotropic and two in the anisotropic Raman spectra and their NCE value decreased with the decrease of EC volume fraction in the binary mixture, and finally disappeared. NCE value and the Fermi resonance constants of EC at different concentrations were calculated from the experimental data.

Investigation of new products of quercetin formed in boiling water via UPLC-Q-TOF-MS-MS analysis

Quercetin is one of most important flavonoids in foods with multi-benefits for human health. The thermal processing is the main food processing approach. Here, the stability of quercetin in boiling water (100 °C) was investigated by UPLC-Q-TOF-MS-MS. With the increasing boiling time, quercetin gradually degraded, and the initial degradation time is 17.57 min and the half-degradation time is 169.72 min. The degradation mechanisms included oxidation, hydroxylation and nucleophilic attack cleavage. Combining the retention time and characteristic fragment ion information of the corresponding standards, the degraded products of quercetin in boiling water were identified as 3,4-dihydroxyphenylglyoxylate, 1,3,5-trihydroxybenzene, 3,4,5-trihydroxybenzoic acid and 2,4,6-trihydroxybenzoic acid. Moreover, 2,3-dihydro-2,3',4',5,7-pentahydroxy-3-oxoflavone, quercetin dimers and quinones were also formed.

Effect of pH on stability of dimer structure of the main protease of coronavirus-2

The viral main protease (M^pro) from a novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a key enzyme essential for viral replication and has become an attractive target for antiviral drug development. The M^pro forms a functional dimer and exhibits a pH-dependent enzyme activity and dimerization. Here, we report a molecular dynamics (MD) investigation to gain insights into the structural stability of the enzyme dimer at neutral and acidic pH. Our data shows larger changes in structure of the protein with the acidic pH than that with the neutral pH. Structural analysis of MD trajectories reveals a substantial increase in intersubunit separation, the loss of domain contacts, binding free energy and interaction energy of the dimer which implies the protein instability and tendency of dimer dissociation at acidic pH. The loss in the interaction energy is mainly driven by electrostatic interactions. We have identified the intersubunit hydrogen-bonding residues involved in the decreased dimer stability. These findings may be helpful for rational drug design and target evaluation against COVID-19.

Generation of soluble, cleaved, well-ordered, native-like dimers of dengue virus 4 envelope protein ectodomain (sE) suitable for vaccine immunogen design

Dengue virus is transmitted by Aedes mosquitoes and dengue is endemic in many regions of the world. Severe dengue results in complications that may lead to death. Although some vaccine candidates are in clinical trials and one vaccine Dengvaxia, with restricted efficacy, is available, there are currently no specific therapies to completely prevent or treat dengue. The dengue virus structural protein E (envelope) exists as a head-to-tail dimer on mature virus, is targeted by broadly neutralizing antibodies and is suitable for developing vaccine immunogens. Here, we have used a redesigned dengue prME expression construct and immunoaffinity chromatography with conformational/quaternary antibody A11 to purify soluble DENV4 sE(A259C) (E ectodomain) dimers from mammalian expression system to ~99 % purity. These dimers retain glycosylation reported for native DENV E, display the three major broadly neutralizing antibody epitopes, and form well-ordered structure. This strategy can be used for developing subunit vaccine candidates against dengue and other flaviviruses.

Electronic transitions in noncovalent BODIPY dimers: TD-DFT study

Theoretical computations have been performed on the absorption spectra of (8-R-TMB)₂ dimers with varying character of substituents at the 8 position (meso) at monomers units (R = NH₂, OH, CH₃, H, COH, CF₃, CN). The obtained results (TD-CAM-B3LYP) show that the first four lower transitions of studied dimers (S₀ → S_i, i = 1-4) are intrinsically linked with delocalized HOMO and LUMO orbitals of the two monomers, which constitute a dimer. For all the dimers, S₀ → S₁ and S₀ → S₃ transitions are strongly forbidden, whereas S₀ → S₂ and S₀ → S₄ are allowed. There is a good agreement between the TD-CAM-B3LYP theory and the simple model of exciton coupling for two identical chromophores with the planes of two moieties, which are stacked upon each other. Intensities of the allowed transitions depend strongly on the nature of the substituent at the meso position. For the dimers with monomer units bearing electron-donor groups, S₀ → S₂ transitions are more intense compared with S₀ → S₄ ones. As the donor properties of the meso substituents diminish and electron acceptor properties enlarge, the intensity of these transitions becomes lower, whereas that of S₀ → S₄ transitions becomes higher. For the dimers with NH₂ and CN substituents, the almost inverse ratio of intensities of the transitions discussed is observed (for example, f = 0.80 and 0.06 (in the case of NH₂) and f = 0.09 and 0.72 (CN) for S₀ → S₂ and S₀ → S₄, respectively). Protonation of the tertiary amine function drastically 'switches off' its electron-donating properties. As a result, the red shift of the bands and redistribution of intensities of the allowed S₀ → S₂ and S₀ → S₄ transitions is predicted for protonated forms of the (8-NH₂-TMB)₂ dimer. This peculiarity can be of especial importance for the design of dimers with a sensor function.

Self-assembling, supramolecular chemistry and pharmacology of amphotericin B: Poly-aggregates, oligomers and monomers

Antifungal drugs such as amphotericin B (AmB) interact with lipids and phospholipids located on fungal cell membranes to disrupt them and create pores, leading to cell apoptosis and therefore efficacy. At the same time, the interaction can also take place with cell components from mammalian cells, leading to toxicity. AmB was selected as a model antifungal drug due to the complexity of its supramolecular chemical structure which can self-assemble in three different aggregation states in aqueous media: monomer, oligomer (also known as dimer) and poly-aggregate. The interplay between AmB self-assembly and its efficacy or toxicity against fungal or mammalian cells is not yet fully understood. To the best of our knowledge, this is the first report that investigates the role of excipients in the supramolecular chemistry of AmB and the impact on its biological activity and toxicity. The monomeric state was obtained by complexation with cyclodextrins resulting in the most toxic state, which was attributed to the greater production of highly reactive oxygen species upon disruption of mammalian cell membranes, a less specific mechanism of action compared to the binding to the ergosterol located in fungal cell membranes. The interaction between AmB and sodium deoxycholate resulted in the oligomeric and poly-aggregated forms which bound more selectively to the ergosterol of fungal cell membranes. NMR combined with XRD studies elucidated the interaction between drug and excipient to achieve the AmB aggregation states, and ultimately, their diffusivity across membranes. A linear correlation between particle size and the efficacy/toxicity ratio was established allowing to modulate the biological effect of the drug and hence, to improve pharmacological regimens. However, particle size is not the only factor modulating the biological response but also the equilibrium of each state which dictates the fraction of free monomeric form available. Tuning the aggregation state of AmB formulations is a promising strategy to trigger a more selective response against fungal cells and to reduce the toxicity in mammalian cells.

Dimeric FAPI with potential for tumor theranostics

Radionuclide-labeled fibroblast activation protein inhibitors (FAPIs) are popular nuclear imaging probes in recent years. It's of great significance for tumor diagnosis and has great potential in tumor treatment. However, optimization of the probes is needed to further increase tumor uptake and prolong tumor retention for improved treatment efficacy and fewer side effects. In this issue of AJNMMI, Moon et al. reported two squaramide coupled FAPI conjugates (DOTA.(SA.FAPi)2 and DOTAGA.(SA.FAPi)2) and labeled them with 68Ga. The resulted tracers showed increased tumor accumulation and persistent retention, which led to an advance in PET imaging. The use of dimeric structures provides a feasible strategy to develop radiotherapeutic analogs of FAP inhibitors.

Design, synthesis, and mechanism study of dimerized phenylalanine derivatives as novel HIV-1 capsid inhibitors

HIV-1 capsid (CA) plays indispensable and multiple roles in the life cycle of HIV-1, become an attractive target in antiviral therapy. Herein, we report the design, synthesis, and mechanism study of a novel series of dimerized phenylalanine derivatives as HIV-1 capsid inhibitors using 2-piperazineone or 2,5-piperazinedione as a linker. The structure-activity relationship (SAR) indicated that dimerized phenylalanines were more potent than monomers of the same chemotype. Further, the inclusion of fluorine substituted phenylalanine and methoxyl substituted aniline was found to be beneficial for antiviral activity. From the synthesized series, Q-c4 was found to be the most potent compound with an EC₅₀ value of 0.57 μM, comparable to PF74. Interestingly, Q-c4 demonstrated a slightly higher affinity to the CA monomer than the CA hexamer, commensurate with its more significant effect in the late-stage of the HIV-1 lifecycle. Competitive SPR experiments with peptides from CPSF6 and NUP153 revealed that Q-c4 binds to the interprotomer pocket of hexameric CA as designed. Single-round infection assays showed that Q-c4 interferes with the HIV-1 life cycle in a dual-stage manner, affecting both pre-and post-integration. Stability assays in human plasma and human liver microsomes indicated that although Q-c4 has improved stability over PF74, this kind of inhibitor still requires further optimization. And the results of the online molinspiration software predicted that Q-c4 has desirable physicochemical properties but some properties still have some violation from the Lipinski rule of five. Overall, the dimerized phenylalanines are promising novel platforms for developing future HIV-1 CA inhibitors with considerable potential for optimization.

Fabrication and measurement of fiber optic localized surface plasmon resonance sensor based on gold nanoparticle dimer

Fiber optic localized surface plasmon resonance (FO LSPR) sensors capable of portable, real-time, and remote sensing are emerging with the progress of lab-on-fiber technology. However, the small area of the substrate by the optical fiber often restricts the sensitivity of the FO LSPR sensors. To improve the performance of the FO LSPR sensors, it is necessary to enhance the interactions between incident light and plasmonic nanostructures within a defined region. Dimer in which two nanoparticles are arranged with nanometer spacing can effectively increase the light-nanostructure interactions. It is well known that the nanogap made in the assembled nanoparticles significantly enhances the intensity of the electromagnetic field in the confined area by the hot spot effect. We fabricate the dimers of gold nanoparticles on the optical fiber with benzenethiol using a method that reduces the repulsive force between the nanoparticles. In the dimers, the strong plasmonic interaction between the two nanoparticles produces a longitudinal plasmon coupling band, which is compared to the transverse plasmon band by the monomer-based FO LSPR sensor with a similar density of gold nanoparticles. In the proposed sensor, the longitudinal band displays approximately 9.1 times improved sensitivity. When two types of sensors are applied to the biosensor application, the dimer-based FO LSPR sensor also proves an improved limit of detection of about 2.6 times. This method is expected to become a milestone in the field of measurement for small molecules and low concentration through the advancement of the yield and density of dimers.

FDTD Study on Evolution of Trimer Silver@Silica Nanospheres to Dimer for SERS Characteristics

Light enhancement occurs strongly within the plasmonic clusters by interaction with surface plasmons. Surface-enhanced Raman spectroscopic (SERS) characteristics of a series of silver@silica trimer core-shell (CS) nanosphere (NS) clusters are investigated in this paper. It is significant to understand the electric field (EF) enhancement mechanism behind the SERS technique. The effect of symmetry breaking is studied for the series starting from the highly symmetric trimer cluster and transformed to linear dimer geometry which progresses through the gradual reduction in the vertex NS. The optical activity such as the evolution of LSPR peak is discussed, the formation of hot spots is demonstrated and the strength of the local EF enhancement is calculated and correlated with the plasmon dipolar modes by using plasmon hybridization theory to understand the underlying physical concepts.

Anticancer properties of bisaminoquinolines with modified linkers

We have previously reported the unique features of dimeric bisaminoquinolines as anticancer agents and have identified their cellular target as PPT1, a protein palmitoyl-thioesterase. We now report a systematic study on the role of the linker in these constructs, both with respect to the distance between the heterocycles, the linker hydrophobicity and the methylation status (primary vs. secondary vs. tertiary) of the central nitrogen atom on the observed biological activity.

Comparison of the degradation of multiple amine-containing pharmaceuticals during electroindirect oxidation and electrochlorination processes in continuous system

The degradation of pharmaceuticals by electrochemical oxidation (EO) in simulated wastewater containing multiple pharmaceuticals was compared between batch and continuous reactors. Despite the excellent efficiencies achieved in batch experiments, the practical/large-scale applications of EO-degrading amine-containing pharmaceuticals has not yet been accomplished. This paper presents the results of continuous experiments with one of the most promising electrochemical configurations of Pt/Ti electrodes before proceeding to application. In the continuous electrooxidation system (without chloride), direct oxidation on the electrode surface and oxidation by hydroxyl radicals were the main pathways. Due to their short lifespans, the radicals could not be transferred to the bulk solution, and the removal of pharmaceuticals followed the order of sulfamethoxazole (SMX) > paracetamol (PAR) > diclofenac (DIC). In the electrochlorination system (with chloride), oxidation by residual chlorine was the main pathway. The removal of pharmaceuticals followed the order of sulfamethoxazole (SMX) > diclofenac (DIC) > paracetamol (PAR). High SMX removal was realized because of the high reaction rate of SMX with free chlorine. Among the pharmaceuticals, PAR had the lowest removal because it is a neutral species with a low mass transfer rate without the attraction of electrostatic force. These results are consistent with the predictions from our previous batch-scale study, which showed that the reaction rate of dissociated compounds could be increased by the addition of electrostatic force. Furthermore, multiple coexisting pharmaceuticals, such as SMX and PAR or DIC, may form dimers that can be transferred to complex structures and cause higher toxicity.

Cannabinoid receptor CB1 and CB2 interacting proteins: Techniques, progress and perspectives

Cannabinoid receptors 1 and 2 (CB₁ and CB₂) are implicated in a range of physiological processes and have gained attention as promising therapeutic targets for a number of diseases. Protein-protein interactions play an integral role in modulating G protein-coupled receptor (GPCR) expression, subcellular distribution and signaling, and the identification and characterization of these will not only improve our understanding of GPCR function and biology, but may provide a novel avenue for therapeutic intervention. A variety of techniques are currently being used to investigate GPCR protein-protein interactions, including Förster/fluorescence and bioluminescence resonance energy transfer (FRET and BRET), proximity ligation assay (PLA), and bimolecular fluorescence complementation (BiFC). However, the reliable application of these methodologies is dependent on the use of appropriate controls and the consideration of the physiological context. Though not as extensively characterized as some other GPCRs, the investigation of CB₁ and CB₂ interacting proteins is a growing area of interest, and a range of interacting partners have been identified to date. This review summarizes the current state of the literature regarding the cannabinoid receptor interactome, provides commentary on the methodologies and techniques utilized, and discusses future perspectives.

Exciton transfer between LH1 antenna complex and photosynthetic reaction center dimer

The exciton transfer between light-harvesting complex 1(LH1) and photosynthetic reaction center dimer is investigated theoretically. We assume a ring shape structure of the LH1 complex with dimer in the ring centre. The kinetic equations which describe the energy transfer between the antenna complex and reaction center dimer were derived. It was shown that the dimer does not act as a photon trap. There is a weak localization of the exciton on the dimer and there is relatively rapid back exciton transfer from dimer to antenna complex which depends on the number of the pigment molecules in the antenna ring. The relation between the rates of the exciton transfer from the antenna complex to dimer and back transfer from dimer to antenna complex has been derived.

The Pathogenesis Mechanism, Structure Properties, Potential Drugs and Therapeutic Nanoparticles against the Small Oligomers of Amyloid-β

Alzheimer's Disease (AD) is a devastating neurodegenerative disease that affects millions of people in the world. The abnormal aggregation of amyloid β protein (Aβ) is regarded as the key event in AD onset. Meanwhile, the Aβ oligomers are believed to be the most toxic species of Aβ. Recent studies show that the Aβ dimers, which are the smallest form of Aβ oligomers, also have the neurotoxicity in the absence of other oligomers in physiological conditions. In this review, we focus on the pathogenesis, structure and potential therapeutic molecules against small Aβ oligomers, as well as the nanoparticles (NPs) in the treatment of AD. In this review, we firstly focus on the pathogenic mechanism of Aβ oligomers, especially the Aβ dimers. The toxicity of Aβ dimer or oligomers, which attributes to the interactions with various receptors and the disruption of membrane or intracellular environments, were introduced. Then the structure properties of Aβ dimers and oligomers are summarized. Although some structural information such as the secondary structure content is characterized by experimental technologies, detailed structures are still absent. Following that, the small molecules targeting Aβ dimers or oligomers are collected; nevertheless, all of these ligands have failed to come into the market due to the rising controversy of the Aβ-related "amyloid cascade hypothesis". At last, the recent progress about the nanoparticles as the potential drugs or the drug delivery for the Aβ oligomers are present.

CuO and TiO2 particles generated more stable and stronger EPFRs in dark than under UV-irradiation

Environmentally persistent free radicals (EFPRs) have recently attracted a great deal of research attention because of their significant toxicity and ubiquitous occurrence in the environment. The information is still very limited on how to estimate the intensity of EPFRs under ambient circumstances. This study is designed to specifically compare EPFRs generation during catechol degradation in dark and UV light irradiation. CuO and TiO₂ were selected as model metal oxides to coat on silica at 1% CuO has a large electron exchange capacity, which may mediate catechol degradation in dark, while TiO₂ possesses strong photocatalytic property and could accelerate catechol degradation under UV light. Under UV light irradiation, EPFRs were generated very quickly and reached the maximum value in 4 d, which was related to the photocatalytic property of the particle. However, these EPFRs dissipated quickly in 14 d. On the contrary, the intensities of EPFRs generated in dark were 2 times higher, and stabled for over 2 months. Therefore, the environmental impacts of EPFRs in dark may be widespread and long-lasting, which should be monitored more carefully. It should be noted that for CuO-coated silica, a significant amount of EPFRs (20% of the maximum) survived the UV-light irradiation and stabled during the experimental period (45 d). Stronger EPFRs were associated with more abundant dimer structures, suggesting the dimer structures were related to EPFRs formation during catechol degradation. Monitoring the generation of dimer structures in the degradation of organic chemicals may provide useful information to estimate EPFRs generation and risks.

Physicochemical characterization of the G51D mutation of α-synuclein that is responsible for its severe cytotoxicity

Fibril formation and aggregation of α-synuclein are important for the pathogenesis of neurodegenerative disorders including Parkinson's disease. In familial Parkinson's disease, the G51D mutation of α-synuclein causes severe symptoms and rapid progression. α-Synuclein, an intrinsically disordered protein, was shown to adopt an α-helical tetrameric state that resists fibrillation and aggregation. Here, we isolated the stable dimeric state of recombinant wild-type (WT) α-synuclein and G51D α-synuclein protein. Using circular dichroism spectroscopy, we determined that the α-synuclein dimer and monomer structures were unfolded. The WT α-synuclein dimer was more resistant to fibril formation than the monomer. However, the fibril formation rate of the G51D α-synuclein dimer was similar to that of the G51D α-synuclein monomer. The fibril morphology and properties of the G51D α-synuclein monomer were different from those of the WT α-synuclein monomer and dimer and G51D α-synuclein dimer. Additionally, G51D α-synuclein monomer fibrils were more cytotoxic than other fibrils. Our findings indicate that the structural differences between G51D α-synuclein monomer fibrils and other fibrils are critically responsible for its severe neurotoxicity in familial Parkinson's disease.

STAT1 N-terminal domain discriminatively controls type I and type II IFN signaling

The seven signal transducers of transcription (STATs) are cytokine-inducible modular transcription factors. They transmit the stimulation of cells with type I interferons (IFN-α/IFN-β) and type II interferon (IFN-ɣ) into altered gene expression patterns. The N-terminal domain (NTD) of STAT1 is a surface for STAT1/STAT1 homodimer and STAT1/STAT2 heterodimer formation and allows the cooperative DNA binding of STAT1. We investigated whether the STAT1 NTD-mediated dimerization affected the IFN-induced tyrosine phosphorylation of STAT1, its nuclear translocation, STAT1-dependent gene expression, and IFN-dependent antiviral defense. We reconstituted human STAT1-negative and STAT2-negative fibrosarcoma cells with STAT1, NTD-mutated STAT1 (STAT1AA), STAT1 with a mutated DNA-binding domain (DBD), or STAT2. We treated these cells with IFN-α and IFN-ɣ to assess differences between IFN-α-induced STAT1 homo- and heterodimers and IFN-ɣ-induced STAT1 homodimers. Our data demonstrate that IFNs induce the phosphorylation of STAT1 and STAT1AA at Y701 and their nuclear accumulation. We further reveal that STAT1AA can be phosphorylated in response to IFN-α in the absence of STAT2 and that IFN-ɣ-induced STAT1AA can activate gene expression directly. However, STAT1AA largely fails to bind STAT2 and to activate IFN-α-induced expression of endogenous antiviral STAT1/STAT2 target proteins. Congruent herewith, both an intact STAT1 NTD and STAT2 are indispensable to establish an antiviral state with IFN-α. These data provide new insights into the biological importance of the STAT1 NTD.

Purification and characterisation of the dimeric group 12 allergen from Blomia tropicalis heterologously expressed by Escherichia coli Top10F´

Successful research in the wide-ranging field of allergy is usually achieved by definition not only of physicochemical and immunological properties of natural, but also recombinant allergens. Blomia tropicalis mite is a well-known source for various groups of hypersensitivity-causing proteins. The goal of the present work was to produce, purify and characterise by in silico, biochemical and immunological methods the recombinant group-12 allergen of B. tropicalis. The recombinant Blo t 12 aggregation capacity as well as the affinity to antibodies from BALB/c immunised mice and B. tropicalis-sensitised human donors were investigated through in silico analyses, dynamic light scattering, SDS-PAGE, ELISA and Western blot. The presence of Blo t 12 within B. tropicalis extracts was also determined by ELISA and Western blot. High concentrations of dimeric rBlo t 12 were detected through SDS-PAGE next to other aggregates and the results were confirmed by data from DLS and Western blot. The YITVM peptide was predicted to be the most aggregation-prone region. The IgE-reactivity of rBlo t 12 was not completely abolished by aggregate formation but it was significantly decreased compared to rBlo t 5, or B. tropicalis extracts. Natural Blo t 12 may naturally dimerises, but it was detected in non-delipidified B. tropicalis extracts in low amounts. Given that this allergen may be a specific marker for B. tropicalis allergy, the recombinant Blo t 12 herein obtained is characterised as a mid-tier allergen in Brazilian atopic patients and may be useful for the improvement in precision allergy molecular diagnostic applications.

Biased signaling: A viable strategy to drug ghrelin receptors for the treatment of obesity

Obesity is a global burden and a chronic ailment with damaging overall health effects. Ghrelin, an octanoylated 28 amino acid peptide hormone, is secreted from the oxyntic mucosa of the stomach. Ghrelin acts on regions of the hypothalamus to regulate feeding behavior and glucose homeostasis through its G protein-coupled receptor. Recently, several central pathways modulating the metabolic actions of ghrelin have been reported. While these signaling pathways can be inhibited or activated by antagonists or agonists, they can also be discriminatingly activated in a "biased" response to impart different degrees of activation in distinct pathways downstream of the receptor. Here, we review recent ghrelin biased signaling findings as well as characteristics of ghrelin hormone and its receptors pertinent for biased signaling. We then evaluate the feasibility for ghrelin receptor biased signaling as a strategy for the development of effective pharmacotherapy in obesity treatment.

Impact of downstream effects of glucocorticoid receptor dysfunction on organ function in critical illness-associated systemic inflammation

Glucocorticoids (GCs) are stress hormones that regulate developmental and physiological processes and are among the most potent anti-inflammatory drugs to suppress chronic and acute inflammation. GCs act through the glucocorticoid receptor (GR), a ubiquitously expressed ligand-activated transcription factor, which translocates into the nucleus and can act via two different modes, as a GR monomer or as a GR dimer. These two modes of action are not clearly differentiated in practice and may lead to completely different therapeutic outcomes. Detailed aspects of GR mechanisms are often not taken into account when GCs are used in different clinical scenarios. Patients, with critical illness-related corticosteroid insufficiency, treated with natural or synthetic GCs are still missing a clearly defined therapeutic strategy. This review discusses the different modes of GR function and its importance on organ function in vivo.

Native disulphide-linked dimers facilitate amyloid fibril formation by bovine milk αS2-casein

Bovine milk α_S2-casein, an intrinsically disordered protein, readily forms amyloid fibrils in vitro and is implicated in the formation of amyloid fibril deposits in mammary tissue. Its two cysteine residues participate in the formation of either intra- or intermolecular disulphide bonds, generating monomer and dimer species. X-ray solution scattering measurements indicated that both forms of the protein adopt large, spherical oligomers at 20 °C. Upon incubation at 37 °C, the disulphide-linked dimer showed a significantly greater propensity to form amyloid fibrils than its monomeric counterpart. Thioflavin T fluorescence, circular dichroism and infrared spectra were consistent with one or both of the dimer isomers (in a parallel or antiparallel arrangement) being predisposed toward an ordered, amyloid-like structure. Limited proteolysis experiments indicated that the region from Ala⁸¹ to Lys¹¹³ is incorporated into the fibril core, implying that this region, which is predicted by several algorithms to be amyloidogenic, initiates fibril formation of α_S2-casein. The partial conservation of the cysteine motif and the frequent occurrence of disulphide-linked dimers in mammalian milks despite the associated risk of mammary amyloidosis, suggest that the dimeric conformation of α_S2-casein is a functional, yet amyloidogenic, structure.

Experimental approach, theoretical investigation and molecular docking of 2- chloro-5-fluoro phenol antibacterial compound

The molecular structural dimerization of biologically potent 2-chloro-5-fluoro phenol (2C5FP) is optimized. A combined experimental and theoretical characteristics of vibrational spectral determinations (NMR, FT-IR and Raman) on 2-chloro-5-fluoro phenol (2C5FP) were used at DFT-B3LYP/6–31++G (d,p) level of computation. A close coherence is achieved when experimentally observed wave numbers are compared with calculated wave numbers by refinement of the scale factors. Calculated values of global chemical descriptors of the present molecule reveal significant molecular stability and chemical reactivity. Non-Linear optical (NLO) property of the present molecule is investigated by determining the second order non linear parameter of first hyperpolarizability β. Moreover, hydrogen bond and thermodynamic parameters at various temperatures are determined and discussed. Investigated compound 2C5FP possesses a better antibacterial activity against Echerichia coli, Streptococcus aureus, Pseudomonas aureus,and Staphylococcus aureus, respectively. The title molecule is subjected to molecular docking studies with two different proteins, namely Staphylococcus aureus Tyrosyl-tRNA synthetase (PDB ID: 1JIL) and human dihydroorotate dehydrogenase (hDHODH) (PDB ID: 6CJF). The results of molecular docking analysis support the antibacterial activity and demonstrate a strong interaction with the DHODH inhibitor.

A method for identifying G protein-coupled receptor dimers and their interfaces

The G protein-coupled receptor (GPCR) dimer interface plays an important role in the formation and stabilization of the dimer. Therefore, identifying the potential receptor-receptor interface is an important part of studying GPCRs. Various strategies have been employed to study the GPCR dimer interface and explore its functional significance, but experimental methods lack robustness and calculations are laborious. Herein, we report a combined optimized experimental and calculation approach for identifying and structurally characterizing GPCR dimer interfaces, and constructing atomic resolution models. Using a transmembrane domain (TM) peptide containing a human immunodeficiency virus trans-acting transcriptional activator (HIV-TAT) protein transduction motif, matrix-assisted laser desorption tandem time-of-flight mass spectrometry (MALDITOF-MS), and bioluminescence resonance energy transfer (BRET), we successfully identified Apelin receptor (APJ)/Nociceptin receptor 1 (ORL1) and APJ/Vasopressin receptor 2 (V2R) heterodimer interfaces, and two key sites mediating dimerization. This method can identify dimer interfaces of GPCR homodimers and heterodimers.

X-ray Crystallography Reveals Parallel and Antiparallel β-Sheet Dimers of a β-Hairpin Derived from Aβ16-36 that Assemble to Form Different Tetramers

High-resolution structures of oligomers formed by the β-amyloid peptide, Aβ, are important for understanding the molecular basis of Alzheimer's disease. Dimers of Aβ are linked to the pathogenesis and progression of Alzheimer's disease, and tetramers of Aβ are neurotoxic. This paper reports the X-ray crystallographic structures of dimers and tetramers, as well as an octamer, formed by a peptide derived from the central and C-terminal regions of Aβ. In the crystal lattice, the peptide assembles to form two different dimers-an antiparallel β-sheet dimer and a parallel β-sheet dimer-that each further self-assemble to form two different tetramers-a sandwich-like tetramer and a twisted β-sheet tetramer. The structures of these dimers and tetramers derived from Aβ serve as potential models for dimers and tetramers of full-length Aβ that form in vitro and in Alzheimer's disease-afflicted brains.

Dimeric small molecule agonists of EphA2 receptor inhibit glioblastoma cell growth

EphA2 receptor kinase could become a novel target for anti-glioblastoma treatment. Doxazosin previously identified acts like the endogenous ligand of EphA2 and induces cell apoptosis. Through lead structure modification a derivative of Doxazosin possessing unique dimeric structure showed an improvement in the activity. In the current study, we expanded the dimeric scaffold by lead optimization to explore the chemical space of the conjoining moieties and a slight variation to the core structure. 27 new derivatives were synthesized and examined with EphA2 overexpressed and wild type glioblastoma cell lines for cell proliferation and EphA2 activation. Three new compounds 3d, 3e, and 7bg showed potent and selective activities against the growth of EphA2 overexpressed glioblastoma cells. Dimer 3d modification replaces the long alkyl chain with a short polyethylene glycol chain. Dimer 7bg has a relatively longer polyethylene glycol chain in comparison to compound 3d and the length is more similar to the lead compound. Whereas dimer 3e has a rigid aromatic linker exploring the chemical space. The diversity of the linkers in the active suggest additional hydrogen binding sites has a positive correlation to the activity. All three dimers showed selective activity in EphA2 overexpressed cells, indicating the activity is correlated to the EphA2 targeting effect.

Structural insights into the formation of oligomeric state by a type I Hsp40 chaperone

Molecular chaperones can prevent and repair protein misfolding and aggregation to maintain protein homeostasis in cells. Hsp40 chaperones interact with unfolded client proteins via the dynamic multivalent interaction (DMI) mechanism with their multiple client-binding sites. Here we report that a type I Hsp40 chaperone from Streptococcus pneumonia (spHsp40) forms a concentration-independent polydispersity oligomer state in solution. The crystal structure of spHsp40 determined at 2.75 Å revealed that each monomer has a type I Hsp40 structural fold containing a zinc finger domain and C-terminal domains I and II (CTD I and CTD II). Subsequent quaternary structure analysis using a PISA server generated two dimeric models. The interface mutational analysis suggests the conserved C-terminal dimeric motif as a basis for dimer formation and that the novel dimeric interaction between a client-binding site in CTD I and the zinc finger domain promotes the formation of the spHsp40 oligomeric state. In vitro functional analysis demonstrated that spHsp40 oligomer is fully active and possess the optimal activity in stimulating the ATPase activity of spHsp70. The oligomer state of type I Hsp40 and its formation might be important in understanding Hsp40 function and its interaction with client proteins.

Partial oxidation of phenol in supercritical water with NaOH and H2O2: Hydrogen production and polymer formation

The catalytic supercritical water partial oxidation of phenol using H₂O₂ as oxidant in the presence of NaOH was explored to enhance hydrogen production and inhibit phenol polymerization. The results indicated that H₂ production was enhanced in the presence of NaOH when phenol supercritical water oxidation was controlled at a lower O/C ratio. Compared with the individual catalytic partial oxidation of phenol, the reaction with NaOH and H₂O₂ simultaneously enhanced H₂ production and inhibited polycyclic polymer generation at O/C ratios below 0.5. A peak hydrogen gasification efficiency value of 62.35% was observed at an O/C ratio of 0.3 with 1.0 wt% NaOH, and a phenol removal efficiency of nearly 75% was reported. Phenol polymerization was effectively inhibited for reaction times limited to 50 s. Moreover, other phenol reaction pathways reported in the literature were compared with the partial oxidation of phenol in supercritical water with NaOH and H₂O₂.

Current scenario of indole derivatives with potential anti-drug-resistant cancer activity

Cancer chemotherapy is frequently hampered by drug resistance, so the resistance to anticancer agents represents one of the major obstacles for the effective cancer treatment. Indole derivatives have the potential to act on diverse targets in cancer cells and exhibit promising activity against drug-resistant cancers. Moreover, some indole-containing compounds such as Semaxanib, Sunitinib, Vinorelbine, and Vinblastine have already been applied in clinics for various kinds of cancer even drug-resistant cancer therapy. Thus, indole derivatives are one of significant resources for the development of novel anti-drug-resistant cancer agents. This review focuses on the recent development of indole derivatives with potential therapeutic application for drug-resistant cancers, and the mechanisms of action, the critical aspects of design as well as structure-activity relationships, covering articles published from 2010 to 2020.

Quantification of residual hydrophobic fusion peptide with monomer and dimer forms using reversed-phase liquid chromatography

A fusion peptide mimicking a part of the sequence of HIV-1 envelope glycoprotein with an additional cysteine at its C-terminus (FP8: AVGIGAVFC) was conjugated to a carrier protein through a linker for development of an HIV-1 vaccine. Since this fusion peptide is very hydrophobic with poor solubility and can self-dimerize via a disulfide bond, co-existence of monomeric and dimeric forms presented a major challenge for residual unconjugated FP8 quantification. A reversed-phase liquid chromatography (RPLC) with UV detection was developed to monitor residual FP8 using an experimental correction factor of 0.85 for UV peak area measurement between FP8 dimer and monomer. Therefore, both forms of unconjugated residual FP8 can be measured based on a single FP8 monomer reference curve. Overall, this study demonstrated that the current purification process can remove free residual FP8 to a low level, <20 µg/mL, which showed negligible impact (<10%) for the conjugated FP8 ratio measurement using another method, amino acid analysis.