Particulate Array of Well-Ordered HIV Clade C Env Trimers Elicits Neutralizing Antibodies that Display a Unique V2 Cap Approach.

The development of soluble envelope glycoprotein (Env) mimetics displaying ordered trimeric symmetry has ushered in a new era in HIV-1 vaccination. The recently reported native, flexibly linked (NFL) design allows the generation of native-like trimers from clinical isolates at high yields and homogeneity. As the majority of infections world-wide are of the clade C subtype, we examined responses in non-human primates to well-ordered subtype C 16055 trimers administered in soluble or high-density liposomal formats. We detected superior germinal center formation and enhanced autologous neutralizing antibodies against the neutralization-resistant (tier 2) 16055 virus following inoculation of liposome-arrayed trimers. Epitope mapping of the neutralizing monoclonal antibodies (mAbs) indicated major contacts with the V2 apex, and 3D electron microscopy reconstructions of Fab-trimer complexes revealed a horizontal binding angle to the Env spike. These vaccine-elicited mAbs target the V2 cap, demonstrating a means to accomplish tier 2 virus neutralization by penetrating the dense N-glycan shield.

The therapeutic potential of indole hybrids, dimers, and trimers against drug-resistant ESKAPE pathogens.

Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter (ESKAPE) species as causative agents are characterized by increased levels of resistance toward multiple classes of first-line as well as last-resort antibiotics and represent serious global health concerns, creating a critical need for the development of novel antibacterials with therapeutic potential against drug-resistant ESKAPE species. Indole derivatives with structural and mechanistic diversity demonstrated broad-spectrum antibacterial activity against various clinically important pathogens including drug-resistant ESKAPE. Moreover, several indole-based agents that are exemplified by creatmycin have already been used in clinics or under clinical trials for the treatment of bacterial infections, demonstrating that indole derivatives hold great promise for the development of novel antibacterials. This review is an endeavor to highlight the current scenario of indole hybrids, dimers, and trimers with therapeutic potential against drug-resistant ESKAPE pathogens, covering articles published from 2020 to the present, to open new avenues for the exploration of novel antidrug-resistant ESKAPE candidates.

Nanoscale Organization of TRAIL Trimers using DNA Origami to Promote Clustering of Death Receptor and Cancer Cell Apoptosis.

Through inducing death receptor (DR) clustering to activate downstream signaling, tumor necrosis factor related apoptosis inducing ligand (TRAIL) trimers trigger apoptosis of tumor cells. However, the poor agonistic activity of current TRAIL-based therapeutics limits their antitumor efficiency. The nanoscale spatial organization of TRAIL trimers at different interligand distances is still challenging, which is essential for the understanding of interaction pattern between TRAIL and DR. In this study, a flat rectangular DNA origami is employed as display scaffold, and an "engraving-printing" strategy is developed to rapidly decorate three TRAIL monomers onto its surface to form DNA-TRAIL3 trimer (DNA origami with surface decoration of three TRAIL monomers). With the spatial addressability of DNA origami, the interligand distances are precisely controlled from 15 to 60 nm. Through comparing the receptor affinity, agonistic activity and cytotoxicity of these DNA-TRAIL3 trimers, it is found that ≈40 nm is the critical interligand distance of DNA-TRAIL3 trimers to induce death receptor clustering and the resulting apoptosis.Finally, a hypothetical "active unit" model is proposed for the DR5 clustering induced by DNA-TRAIL3 trimers.

Laser-Induced Coulomb Explosion Imaging of Aligned Molecules and Molecular Dimers.

We discuss how Coulomb explosion imaging (CEI), triggered by intense femtosecond laser pulses and combined with laser-induced alignment and covariance analysis of the angular distributions of the recoiling fragment ions, provides new opportunities for imaging the structures of molecules and molecular complexes. First, focusing on gas phase molecules, we show how the periodic torsional motion of halogenated biphenyl molecules can be measured in real time by timed CEI, and how CEI of one-dimensionally aligned difluoroiodobenzene molecules can uniquely identify four structural isomers. Next, focusing on molecular complexes formed inside He nano-droplets, we show that the conformations of noncovalently bound dimers or trimers, aligned in one or three dimensions, can be determined by CEI. Results presented for homodimers of CS2, OCS, and bromobenzene pave the way for femtosecond time-resolved structure imaging of molecules undergoing bimolecular interactions and ultimately chemical reactions.

Enhancement of Neutralization Responses through Sequential Immunization of Stable Env Trimers Based on Consensus Sequences from Select Time Points by Mimicking Natural Infection.

HIV-1 vaccines have been challenging to develop, partly due to the high level of genetic variation in its genome. Thus, a vaccine that can induce cross-reactive neutralization activities will be needed. Studies on the co-evolution of antibodies and viruses indicate that mimicking the natural infection is likely to induce broadly neutralizing antibodies (bnAbs). We generated the consensus Env sequence for each time point in subject CH505, who developed broad neutralization activities, and selected five critical time points before broad neutralization was detected. These consensus sequences were designed to express stable Env trimers. Priming with the transmitted/founder Env timer and sequential boosting with these consensus Env trimers from different time points induced broader and more potent neutralizing activities than the BG505 Env trimer in guinea pigs. Analysis of the neutralization profiles showed that sequential immunization of Env trimers favored nAbs with gp120/gp41 interface specificity while the BG505 Env trimer favored nAbs with V2 specificity. The unique features such as consensus sequences, stable Env trimers and the sequential immunization to mimic natural infection likely has allowed the induction of improved neutralization responses.

Production and Study of Immunochemical Properties of Stabilized Env Trimer of Recombinant Form CRF63_02A6 of HIV-1.

Stabilized trimers of the HIV-1 envelope glycoprotein Env are capable of inducing a potent and sustained broadly neutralizing antibody response in laboratory animals and therefore are attractive targets for anti-HIV vaccine development. In this work, a stable producer of the trimer Env recombinant form CRF63_02A6 of HIV-1 was derived from the CHO-K1 cell line. Using immunochemical assays, the trimers synthesized in CHO-K1 cells were shown to be recognized by both monoclonal broadly neutralizing antibodies and sera from HIV-positive patients. The resulting trimers of the recombinant form CRF63_02A6 of HIV-1 can be used both for structural studies and as a candidate vaccine immunogen against HIV-1.

Mixed-Valence BN-Doped Corannulene Trimer Radical Cations.

Mixed-valence (MV) dimers have been extensively investigated, however, the structure and properties of purely organic MV trimers based on open-shell polycyclic aromatic hydrocarbons remain elusive. Herein, unprecedented MV BN-doped corannulene radical cations [BN-Cor1]3 ⋅⋅2+ ⋅ 2[BArylF 4 ]- and [BN-Cor2]3 ⋅⋅2+ ⋅ 2[BArylF 4 ]- were synthesized via chemical oxidation, and their structures were unambiguously confirmed by single-crystal X-ray diffraction. These uncommon radical cations consist of three corannulene cores and two [BArylF 4 ]- anions, and three corannulene motifs [BN-Cor1]3 ⋅⋅2+ and [BN-Cor2]3 ⋅⋅2+ in the unit cell exhibit a trimer structure with a slipped π-stacking configuration. Detailed structural analyses further revealed that the corannulene cores exhibit an infinite layered self-assembly configuration, allowing their potential applications as building blocks for molecular conductors. The detection of a forbidden transition (Δms =±2) by electron paramagnetic resonance (EPR) spectroscopy further confirmed the existence of two unpaired electrons in the π-trimers and the MV characteristic of these two species. Variable-temperature EPR and conductivity measurements suggested that the BN-doped π-trimers exhibited antiferromagnetic coupling and conductivity properties.

Development of a p72 trimer-based colloidal gold strip for detection of antibodies against African swine fever virus.

African swine fever virus (ASFV) causes a highly contagious and often lethal swine viral disease, and leads to tremendous economic losses to the swine industry. Unfortunately, there are no vaccines and effective antiviral agents available to prevent and control ASFV outbreaks. Therefore, it is necessary to develop simple and rapid strategies to monitor ASFV-infected pigs to restrain its spread. In the current study, ASFV capsid protein p72 was expressed along with its chaperone pB602L to form trimers in human embryonic kidney 293 (HEK293) cells. The p72 trimers were subsequently labeled with colloidal gold to develop a immunochromatographic strip. The strip showed high specificity to ASFV-positive serum and no cross-reactivity to other swine virus positive sera. Importantly, the strip showed a higher sensitivity of detecting ASFV antibodies in both positive standard serum and clinical serum samples than a commercial enzyme-linked immunosorbent assay (ELISA) kit. Taken together, these results demonstrate the strip as a reliable diagnostic tool against ASFV infection, which will be appropriate for application in prevention and control of ASFV. KEY POINTS : • ASFV p72 trimers were successfully generated. • A colloidal gold strip was developed based on ASFV p72 trimers. • The strip is appropriate for detecting ASFV antibodies in the field.

(±)-Cryptamides A-D, Four Pairs of Novel Dopamine Enantiomer Trimers from the Periostracum Cicadae.

Four pairs of novel dopamine enantiomer trimers, (±)-cryptamides A-D (1-4), and 10 pairs of previously described dopamine enantiomer dimers (5-14) were isolated from the Periostracum cicadae, the cast-off shell of the insect Cryptotympana pustulata. Aside from being pairs of enantiomers, the eight trimers were also elucidated to be regioisomers, most likely resulting from their mechanism of formation, [4 + 2] cycloaddition. The discovery of dopamine trimers is rarely reported when it comes to natural products derived from insects.

Novel Cofacial Porphyrin-Based Homo- and Heterotrimetallic Complexes of Transition Metals.

We present a straightforward and generally applicable synthesis route for cofacially linked homo- and heterotrimetallic trisporphyin complexes. The protocol encompasses synthesising the first aryl-based, trans-o-phenylene trisporphyrin starting from pyrrole and benzaldehyde with an overall yield of 3.6 %. It also allows investigating the respective cis-isomer as the first conformationally restricted planar-chiral trisporphyrin. The free-base ligand was used in subsequent metalation reactions to afford the corresponding homotrimetallic Mn(III)-, Fe(III)-, Ni(II)-, Cu(II)-, Zn(II)- and Pd(II) complexes - additionally, a small adaptation of the protocol resulted in the defined Ni(II)Fe(III)Ni(II) complex in a total yield of 2.3 %. By monitoring Ni(II) insertion into the empty trimeric ligands, we affirmed that the outer porphyrin rings are filled before the internal ring. The molecular species were characterised by 1 H NMR, UV-Vis, photoluminescence, IR, MS, CID, and high-resolution IMS measurements.

Acylphloroglucinol trimers from Callistemon salignus seeds: Isolation, configurational assignment, hAChE inhibitory effects, and molecular docking studies.

Alzheimer's disease (AD) diagnoses are greatly increasing in frequency as the global population ages, highlighting an urgent need for new anti-AD strategies. With the aim to search for human acetylcholinesterase (hAChE) inhibitors from the species of Myrtaceae family, ten acylphloroglucinol trimers (APTs), including eight new APTs, callistemontrimers A-H (1a, 1b, 2a, 2b, 3a, 3b, 4b, and 5b), and two naturally occurring ones (4a and 5a), along with one reported triketone-acylphloroglucinol-monoterpene adduct (6), were obtained and structurally characterized from the hAChE inhibitory acetone extract of Callistemon salignus seeds. The structures and their absolute configurations for new APTs were unequivocally established via the detailed interpretation of extensive spectroscopic data (HRESIMS and NMR), ECD calculations, and single crystal X-ray diffraction, whereas the absolute configurations of known APTs were determined by further chiral separation, and calculated ECD calculations. The results of hAChE inhibitory assay revealed that an enantiomeric mixture of 2a/2b, 2a, and 2b are good hAChE inhibitors with IC50 values of 1.22 ±â€¯0.23, 2.28 ±â€¯0.19, and 4.96 ±â€¯0.39 µM, respectively. Molecular docking was used to uncover the modes of interactions for bioactive compounds with the active site of hAChE. In addition, 2 and 6 displayed moderate neurite outgrowth-promoting effects with differentiation rates of 6.16% and 6.19% at a concentration of 1.0 µM, respectively.

Crystal Structure and Magnetic Properties of Trinuclear Transition Metal Complexes (MnII, CoII, NiII and CuII) with Bridging Sulfonate-Functionalized 1,2,4-Triazole Derivatives.

Here we present the synthesis, structure and magnetic properties of complexes of general formula (Mn)(Me2NH2)4][Mn3(µ-L)6(H2O)6] and (Me2NH2)6[M3(µ-L)6(H2O)6] (M = CoII, NiII and CuII); L-2 = 4-(1,2,4-triazol-4-yl) ethanedisulfonate). The trinuclear polyanions were isolated as dimethylammonium salts, and their crystal structures determined by single crystal and powder X-ray diffraction data. The polyanionic part of these salts have the same molecular structure, which consists of a linear array of metal(II) ions linked by triple N1-N2-triazole bridges. In turn, the composition and crystal packing of the MnII salt differs from the rest of the complexes (with six dimethyl ammonia as countercations) in containing one Mn+2 and four dimethyl ammonia as countercations. Magnetic data indicate dominant intramolecular antiferromagnetic interactions stabilizing a paramagnetic ground state. Susceptibility data have been successfully modeled with a simple isotropic Hamiltonian for a centrosymmetric linear trimer, H = -2J (S1S2 + S2S3) with super-exchange parameters J = -0.4 K for MnII, -7.5 K for NiII and -45 K for CuII complex. The magnetic properties of these complexes and their easy processing opens unique possibilities for their incorporation as magnetic molecular probes into such hybrid materials as magnetic/conducting multifunctional materials or as dopant for organic conducting polymers.

Native-like Env trimers as a platform for HIV-1 vaccine design.

We describe the development and potential use of various designs of recombinant HIV-1 envelope glycoprotein trimers that mimic the structure of the virion-associated spike, which is the target for neutralizing antibodies. The goal of trimer development programs is to induce broadly neutralizing antibodies with the potential to intervene against multiple circulating HIV-1 strains. Among the topics we address are the designs of various constructs; how native-like trimers can be produced and purified; the properties of such trimers in vitro and their immunogenicity in various animals; and the immunization strategies that may lead to the eventual elicitation of broadly neutralizing antibodies. In summary, native-like trimers are a now a platform for structure- and immunology-based design improvements that could eventually yield immunogens of practical value for solving the long-standing HIV-1 vaccine problem.

Human Cellular Retinol Binding Protein II Forms a Domain-Swapped Trimer Representing a Novel Fold and a New Template for Protein Engineering.

Domain-swapping is a mechanism for evolving new protein structure from extant scaffolds, and has been an efficient protein-engineering strategy for tailoring functional diversity. However, domain swapping can only be exploited if it can be controlled, especially in cases where various folds can coexist. Herein, we describe the structure of a domain-swapped trimer of the iLBP family member hCRBPII, and suggest a mechanism for domain-swapped trimerization. It is further shown that domain-swapped trimerization can be favored by strategic installation of a disulfide bond, thus demonstrating a strategy for fold control. We further show the domain-swapped trimer to be a useful protein design template by installing a high-affinity metal binding site through the introduction of a single mutation, taking advantage of its threefold symmetry. Together, these studies show how nature can promote oligomerization, stabilize a specific oligomer, and generate new function with minimal changes to the protein sequence.

SOS and IP Modifications Predominantly Affect the Yield but Not Other Properties of SOSIP.664 HIV-1 Env Glycoprotein Trimers.

Soluble recombinant native-like (NL) envelope glycoprotein (Env) trimers of various human immunodeficiency virus type 1 (HIV-1) genotypes are being developed as vaccine candidates aimed at the induction of broadly neutralizing antibodies (bNAbs). The prototypic design, designated BG505 SOSIP.664, incorporates an intersubunit disulfide bond (SOS) to covalently link the gp120 and gp41 ectodomain (gp41ECTO) subunits and a point substitution, I559P (IP), to further stabilize the gp41ECTO components. Without the SOS and IP changes, proteolytically cleaved trimers tend to disintegrate into their constituent gp120 and gp41ECTO subunits. We show, however, that NL trimers lacking the SOS and/or IP change can be affinity purified in amounts sufficient for analyses of their antigenicity and thermal stability. In general, these trimer variants have properties highly comparable to those of the fully stabilized SOSIP.664 version. We conclude that the major effect of the SOS and IP changes is to substantially increase trimer stability during and after the expression process, thereby allowing useful amounts to be produced. However, once the trimers have been purified, the SOS and IP changes have only subtle impacts on thermostability and the antigenicity of bNAb and other epitopes.IMPORTANCE Recombinant trimeric proteins based on HIV-1 env genes are being developed for vaccine trials in humans. A feature of these proteins is their mimicry of the envelope glycoprotein structure on virus particles that is targeted by neutralizing antibodies, i.e., antibodies that prevent cells from becoming infected. One vaccine concept under exploration is that recombinant trimers may be able to elicit virus-neutralizing antibodies when delivered as immunogens. A commonly used design is designated SOSIP.664, a term reflecting the sequence changes that are used to stabilize the trimers and allow their production in practically useful amounts. Here, we show that these stabilizing changes act to increase trimer yield during the biosynthesis process within the producer cell but have little impact on the properties of purified trimers.

Multi-Photochromic Molecules Based on Dihydroazulene Units.

Multi-photochromic systems incorporating individually addressable switching units are attractive for development of advanced data storage devices. Here, we present the synthesis and properties of a selection of such molecular systems incorporating the dihydroazulene/vinylheptafulvene (DHA/VHF) photo-/thermoswitch. The influence of the linker (meta-phenylene vs. azulene-1,3-diyl vs. thiophene-2,5-diyl) separating two DHA units on the switching properties was investigated. An azulene-1,3-diyl spacer largely inhibited both the DHA-to-VHF photoisomerizations and the thermal VHF-to-DHA back-reactions; the latter occurred ten times slower than for the related compound with a meta-phenylene spacer. A DHA trimer containing three DHA units around a central benzene ring was found to undergo stepwise DHA-to-VHF photoisomerizations, whereas the thermal back-reactions occurred at similar rates for the three VHF entities. A meta-phenylene-bridged DHA dimer was subjected to further structural modifications at position C-1 of each DHA, having strong implications for the switching events, and synthetic steps for further functionalizations at position C-7 of each DHA were investigated. Finally, the molecular structure (from X-ray crystallographic analysis) between the meta-phenylene-bridged DHA dimer and CuI is presented.

N-Bridged Acyclic Trimeric Poly-Cyclodiphosphazanes: Highly Tuneable Cyclodiphosphazane Building Blocks.

We have synthesized a completely new family of acyclic trimeric cyclodiphosphazane compounds comprising NH, Ni Pr, Nt Bu and NPh bridging groups. In addition, the first NH-bridged acyclic dimeric cyclophosphazane has been produced. The trimeric species display highly tuneable characteristics so that the distance between the terminal N(H)R moieties can be readily modulated by the steric bulk present in the bridging groups (ranging from ≈6 to ≈10 Å). Moreover, these species exhibit pronounced topological changes when a weak non-bonding NH⋅⋅⋅π aryl interaction is introduced. Finally, the NH-bridged chloride binding affinities have been calculated and benchmarked along with the existing experimental data available for monomeric cyclodiphosphazanes. Our results underscore these species as promising hydrogen bond donors for supramolecular host-guest applications.

Structures and Structural Evolution of Sublayer Surfaces of Metal-Organic Frameworks.

The structural characterization of sublayer surfaces of MIL-101 is reported by low-dose spherical aberration-corrected high-resolution transmission electron microscopy (HRTEM). The state-of-the-art microscopy directly images atomic/molecular configurations in thin crystals from charge density projections, and uncovers the structures of sublayer surfaces and their evolution to stable surfaces regulated by inorganic Cr3 (µ3 -O) trimers. This study provides compelling evidence of metal-organic frameworks (MOFs) crystal growth via the assembly of sublayer surfaces and has important implications in understanding the crystal growth and surface-related properties of MOFs.

Effects of Adjuvants on HIV-1 Envelope Glycoprotein SOSIP Trimers In Vitro.

Native-like, soluble, recombinant SOSIP trimers of various designs and based on several env genes of human immunodeficiency virus type 1 (HIV-1) are being tested as immunogens in different animal models. These experiments almost always involve coformulating the trimers with an adjuvant to boost the magnitude of the immune responses. One factor relevant to the choice of an adjuvant is that it should not physically damage the immunogen or impede its ability to present relevant epitopes. As examples, an adjuvant formulation that includes harsh detergents could disrupt the structural integrity of a trimer, and any charged compounds in the formulation could bind to countercharged regions of the trimer and physically occlude nearby epitopes. While a few adjuvants have been tested for their potential effects on SOSIP trimers in vitro, there has been no systematic study. Here, we have assessed how nine different adjuvants of various compositions affect SOSIP trimers of the BG505 and B41 genotypes. We used negative-stain electron microscopy, thermal denaturation, and gel electrophoresis to evaluate effects on trimer integrity and immunoassays to measure effects on the presentation of various epitopes. We conclude that most of the tested adjuvants are benign from these perspectives, but some raise grounds for concern. An acidified alum formulation is highly disruptive to trimer integrity, and a DNA-based polyanionic CpG oligodeoxynucleotide adjuvant binds to trimers and occludes the trimer apex epitope for the PGT145 neutralizing antibody. The methods described here should be generalizable to protein subunit vaccines targeting various pathogens.IMPORTANCE Adjuvant formulations increase the magnitude of immune responses to vaccine antigens. They are critically important for formulation of HIV-1 envelope glycoprotein (Env) vaccines intended to induce antibody production, as Env proteins are otherwise only very weakly immunogenic. The HIV-1 vaccine field now uses the well-defined structures of trimeric Env glycoproteins, like SOSIPs, to present multiple known epitopes for broad and potent neutralizing human antibodies in a native-like conformation. Successful adjuvant formulations must not disrupt how the trimers are folded, as that could adversely affect their performance as immunogens. We studied whether the various adjuvants most commonly used in animal experiments affect the integrity of two different SOSIP trimers in vitro Most adjuvant classes are not problematic, but an aluminum sulfate formulation is highly damaging, as it exposes trimers to acidic pH and a nucleic acid-based adjuvant can bind to the trimer and block access to a key neutralizing epitope.

[LC-MS guided isolation of two anti-inflammatory cyclic dihydrochalcane trimers from Chinese dragon's blood].

As an important integral part of traditional Chinese medicine chemical biology( TCMCB),it is of great importance to rapid isolate,and reliably identify the chemical components in herbal medicines. Phytochemical studies on the anti-inflammatory active part of Chinese dragon's blood,the red resin of Dracaena cochinchinensis,resulted in the isolation of two compounds,nordracophane( 1) and dracophane( 2),using LC-MS and chromatographic techniques( Silica gel,ODS and preparative HPLC). The structures,cyclic dihydrochalcane trimers,were elucidated on the basis of 1 D and 2 D NMR,MS,IR and UV spectral analysis. Compound 1 is a new compound,and 2 is isolated from D. cochinchinensis for the first time. Both compounds exhibited significant inhibition of nitric oxide production in lipopolysaccharides( LPS)-stimulated RAW264. 7 cells with IC50 values of( 14. 9±4. 50) and( 9. 0±0. 7) µmol·L-1.