Vaccination induces broadly neutralizing antibody precursors to HIV gp41.

A key barrier to the development of vaccines that induce broadly neutralizing antibodies (bnAbs) against human immunodeficiency virus (HIV) and other viruses of high antigenic diversity is the design of priming immunogens that induce rare bnAb-precursor B cells. The high neutralization breadth of the HIV bnAb 10E8 makes elicitation of 10E8-class bnAbs desirable; however, the recessed epitope within gp41 makes envelope trimers poor priming immunogens and requires that 10E8-class bnAbs possess a long heavy chain complementarity determining region 3 (HCDR3) with a specific binding motif. We developed germline-targeting epitope scaffolds with affinity for 10E8-class precursors and engineered nanoparticles for multivalent display. Scaffolds exhibited epitope structural mimicry and bound bnAb-precursor human naive B cells in ex vivo screens, protein nanoparticles induced bnAb-precursor responses in stringent mouse models and rhesus macaques, and mRNA-encoded nanoparticles triggered similar responses in mice. Thus, germline-targeting epitope scaffold nanoparticles can elicit rare bnAb-precursor B cells with predefined binding specificities and HCDR3 features.

Ultrapotent influenza hemagglutinin fusion inhibitors developed through SuFEx-enabled high-throughput medicinal chemistry.

Seasonal and pandemic-associated influenza strains cause highly contagious viral respiratory infections that can lead to severe illness and excess mortality. Here, we report on the optimization of our small-molecule inhibitor F0045(S) targeting the influenza hemagglutinin (HA) stem with our Sulfur-Fluoride Exchange (SuFEx) click chemistry-based high-throughput medicinal chemistry (HTMC) strategy. A combination of SuFEx- and amide-based lead molecule diversification and structure-guided design led to identification and validation of ultrapotent influenza fusion inhibitors with subnanomolar EC50 cellular antiviral activity against several influenza A group 1 strains. X-ray structures of six of these compounds with HA indicate that the appended moieties occupy additional pockets on the HA surface and increase the binding interaction, where the accumulation of several polar interactions also contributes to the improved affinity. The compounds here represent the most potent HA small-molecule inhibitors to date. Our divergent HTMC platform is therefore a powerful, rapid, and cost-effective approach to develop bioactive chemical probes and drug-like candidates against viral targets.

Affinity gaps among B cells in germinal centers drive the selection of MPER precursors.

Current prophylactic human immunodeficiency virus 1 (HIV-1) vaccine research aims to elicit broadly neutralizing antibodies (bnAbs). Membrane-proximal external region (MPER)-targeting bnAbs, such as 10E8, provide exceptionally broad neutralization, but some are autoreactive. Here, we generated humanized B cell antigen receptor knock-in mouse models to test whether a series of germline-targeting immunogens could drive MPER-specific precursors toward bnAbs. We found that recruitment of 10E8 precursors to germinal centers (GCs) required a minimum affinity for germline-targeting immunogens, but the GC residency of MPER precursors was brief due to displacement by higher-affinity endogenous B cell competitors. Higher-affinity germline-targeting immunogens extended the GC residency of MPER precursors, but robust long-term GC residency and maturation were only observed for MPER-HuGL18, an MPER precursor clonotype able to close the affinity gap with endogenous B cell competitors in the GC. Thus, germline-targeting immunogens could induce MPER-targeting antibodies, and B cell residency in the GC may be regulated by a precursor-competitor affinity gap.

Layout Dependence Stress Investigation in through Glass via Interposer Architecture Using a Submodeling Simulation Technique and a Factorial Design Approach.

The multi-chiplet technique is expected to be a promising solution to achieve high-density system integration with low power consumption and high usage ratio. This technique can be integrated with a glass interposer to accomplish a competitive low fabrication cost compared with the silicon-based interposer architecture. In this study, process-oriented stress simulation is performed by the element activation and deactivation technique in finite element analysis architecture. The submodeling technique is also utilized to mostly conquer the scale mismatch and difficulty in mesh gridding design. It is also used to analyze the thermomechanical responses of glass interposers with chiplet arrangements and capped epoxy molding compounds (EMC) during curing. A three-factor, three-level full factorial design is applied using the analysis of variance method to explore the significance of various structural design parameters for stress generation. Analytic results reveal that the maximum first principal stresses of 130.75 and 17.18 MPa are introduced on the sidewall of Cu-filled via and the bottom of the glass interposer, respectively. Moreover, the EMC thickness and through glass via pitch are the dominant factors in the adopted vehicle. They significantly influence the stress magnitude during heating and cooling.

Morphological Diagram of Dynamic-Interfacial-Release-Induced Surface Instability.

In this study, a morphological diagram was constructed for quantitatively predicting various modes of surface instabilities caused by the dynamic interfacial release of strain in initially flat bilayer composites comprising an elastomer and a capping layer. Theory, experiment, and simulation were combined to produce the diagram, which enables systematic generation of the following instability patterns: wrinkle, fold, period-double, delamination, and coexisting patterns. The pattern that forms is most strongly affected by three experimental parameters: the elastic modulus of the elastomer, the elastic modulus of the capping layer, and the thickness of the capping layer. The morphological diagram offers understanding of the formation of complex patterns and development of their applications. Critically, the wrinkle alignment can be well controlled by changing the direction of the interfacial release to enable the creation of centimeter-sized and highly ordered lamellar wrinkled patterns with a single orientation on a soft elastomer without the need for costly high-vacuum instruments or complex fabrication processes. The method and diagram have great potential for broad use in many practical applications ranging from flexible electronic devices to smart windows.

Starfish-Inspired Diamond-Structured Calcite Single Crystals from a Bottom-up Approach as Mechanical Metamaterials.

Inspired by knobby starfish, this work demonstrates a bottom-up approach for fabricating a calcite single-crystal (CSC) with a diamond structure by exploiting the self-assembly of the block copolymer and corresponding templated synthesis. Similar to the knobby starfish, the diamond structure of the CSC gives rise to a brittle-to-ductile transition. Most interestingly, the diamond-structured CSC fabricated exhibits exceptional specific energy absorption and strength with lightweight character superior to natural materials and artificial counterparts from a top-down approach due to the nanosized effect. This approach provides the feasibility for creating mechanical metamaterials with the combined effects of the topology and nanosize on the mechanical performance.

Rare, convergent antibodies targeting the stem helix broadly neutralize diverse betacoronaviruses.

Humanity has faced three recent outbreaks of novel betacoronaviruses, emphasizing the need to develop approaches that broadly target coronaviruses. Here, we identify 55 monoclonal antibodies from COVID-19 convalescent donors that bind diverse betacoronavirus spike proteins. Most antibodies targeted an S2 epitope that included the K814 residue and were non-neutralizing. However, 11 antibodies targeting the stem helix neutralized betacoronaviruses from different lineages. Eight antibodies in this group, including the six broadest and most potent neutralizers, were encoded by IGHV1-46 and IGKV3-20. Crystal structures of three antibodies of this class at 1.5-1.75-Å resolution revealed a conserved mode of binding. COV89-22 neutralized SARS-CoV-2 variants of concern including Omicron BA.4/5 and limited disease in Syrian hamsters. Collectively, these findings identify a class of IGHV1-46/IGKV3-20 antibodies that broadly neutralize betacoronaviruses by targeting the stem helix but indicate these antibodies constitute a small fraction of the broadly reactive antibody response to betacoronaviruses after SARS-CoV-2 infection.

Bioinspired Nanonetwork Hydroxyapatite from Block Copolymer Templated Synthesis for Mechanical Metamaterials.

Inspired by Mantis shrimp, this work aims to suggest a bottom-up approach for the fabrication of nanonetwork hydroxyapatite (HAp) thin film using self-assembled polystyrene-block-polydimethylsiloxane (PS-b-PDMS) block copolymer (BCP) with a diamond nanostructure as a template for templated sol-gel reaction. By introducing poly(vinylpyrrolidone) (PVP) into precursors of calcium nitrate tetrahydrate and triethyl phosphite, which limits the growth of forming HAp nanoparticles, well-ordered nanonetwork HAp thin film can be fabricated. Based on nanoindentation results, the well-ordered nanonetwork HAp shows high energy dissipation compared to the intrinsic HAp. Moreover, the uniaxial microcompression test for the nanonetwork HAp shows high energy absorption per volume and high compression strength, outperforming many cellular materials due to the topologic effect of the well-ordered network at the nanoscale. This work highlights the potential of exploiting BCP templated synthesis to fabricate ionic solid materials with a well-ordered nanonetwork monolith, giving rise to the brittle-to-ductile transition, and thus appealing mechanical properties with the character of mechanical metamaterials.

Reliability Assessment of Thermocompressed Epoxy Molding Compound through Glass via Interposer Architecture by the Submodeling Simulation Approach.

In glass interposer architecture and its assembly process, the mechanical responses of interposer structure under thermocompression process-induced thermal loading and generated shrinkage of molding material are regarded as a major reliability issue. Thousands of metal-filled via are involved in glass interposers and are regarded as a potential risk that can lead to cracking and the failure of an entire vehicle. In this study, a finite element-based submodeling approach is demonstrated to overcome the complexity of modeling and the relevant convergence issue of interposer architecture. Convergence analysis results revealed that at least four via pitch-wide regions of a local simulation model were needed to obtain the stable results enabled by the submodeling simulation approach. The stress-generation mechanism during thermocompression, the coefficient of thermal expansion mismatch, and the curing process-induced shrinkage were separately investigated. The critical stress location was explored as the outer corner of the chip, and the maximum first principal stress during the thermocompression process generated on the chip and glass interposer were 34 and 120 MPa, respectively.

Broadly neutralizing antibodies target the coronavirus fusion peptide.

The potential for future coronavirus outbreaks highlights the need to broadly target this group of pathogens. We used an epitope-agnostic approach to identify six monoclonal antibodies that bind to spike proteins from all seven human-infecting coronaviruses. All six antibodies target the conserved fusion peptide region adjacent to the S2' cleavage site. COV44-62 and COV44-79 broadly neutralize alpha- and betacoronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariants BA.2 and BA.4/5, albeit with lower potency than receptor binding domain-specific antibodies. In crystal structures of COV44-62 and COV44-79 antigen-binding fragments with the SARS-CoV-2 fusion peptide, the fusion peptide epitope adopts a helical structure and includes the arginine residue at the S2' cleavage site. COV44-79 limited disease caused by SARS-CoV-2 in a Syrian hamster model. These findings highlight the fusion peptide as a candidate epitope for next-generation coronavirus vaccine development.

Neutralizing Antibody Response to Sarbecovirus Is Delayed in Sequential Heterologous Immunization.

Antigenic imprinting, which describes the bias of the antibody response due to previous immune history, can influence vaccine effectiveness. While this phenomenon has been reported for viruses such as influenza, there is little understanding of how prior immune history affects the antibody response to SARS-CoV-2. This study provides evidence for antigenic imprinting through immunization with two Sarbecoviruses, the subgenus that includes SARS-CoV-2. Mice were immunized subsequently with two antigenically distinct Sarbecovirus strains, namely SARS-CoV-1 and SARS-CoV-2. We found that sequential heterologous immunization induced cross-reactive binding antibodies for both viruses and delayed the emergence of neutralizing antibody responses against the booster strain. Our results provide fundamental knowledge about the immune response to Sarbecovirus and important insights into the development of pan-sarbecovirus vaccines and guiding therapeutic interventions.

Broadly neutralizing antibodies target the coronavirus fusion peptide.

The potential for future coronavirus outbreaks highlights the need to develop strategies and tools to broadly target this group of pathogens. Here, using an epitope-agnostic approach, we identified six monoclonal antibodies that bound to spike proteins from all seven human-infecting coronaviruses. Epitope mapping revealed that all six antibodies target the conserved fusion peptide region adjacent to the S2' cleavage site. Two antibodies, COV44-62 and COV44-79, broadly neutralize a range of alpha and beta coronaviruses, including SARS-CoV-2 Omicron subvariants BA.1 and BA.2, albeit with lower potency than RBD-specific antibodies. In crystal structures of Fabs COV44-62 and COV44-79 with the SARS-CoV-2 fusion peptide, the fusion peptide epitope adopts a helical structure and includes the arginine at the S2' cleavage site. Importantly, COV44-79 limited disease caused by SARS-CoV-2 in a Syrian hamster model. These findings identify the fusion peptide as the target of the broadest neutralizing antibodies in an epitope-agnostic screen, highlighting this site as a candidate for next-generation coronavirus vaccine development. One-Sentence Summary: Rare monoclonal antibodies from COVID-19 convalescent individuals broadly neutralize coronaviruses by targeting the fusion peptide.

Neutralizing Antibodies to SARS-CoV-2 Selected from a Human Antibody Library Constructed Decades Ago.

Combinatorial antibody libraries not only effectively reduce antibody discovery to a numbers game, but enable documentation of the history of antibody responses in an individual. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has prompted a wider application of this technology to meet the public health challenge of pandemic threats in the modern era. Herein, a combinatorial human antibody library constructed 20 years before the coronavirus disease 2019 (COVID-19) pandemic is used to discover three highly potent antibodies that selectively bind SARS-CoV-2 spike protein and neutralize authentic SARS-CoV-2 virus. Compared to neutralizing antibodies from COVID-19 patients with generally low somatic hypermutation (SHM), these three antibodies contain over 13-22 SHMs, many of which are involved in specific interactions in their crystal structures with SARS-CoV-2 spike receptor binding domain. The identification of these somatically mutated antibodies in a pre-pandemic library raises intriguing questions about the origin and evolution of these antibodies with respect to their reactivity with SARS-CoV-2.

Stress Impact of the Annealing Procedure of Cu-Filled TSV Packaging on the Performance of Nano-Scaled MOSFETs Evaluated by an Analytical Solution and FEA-Based Submodeling Technique.

Stress-induced performance change in electron packaging architecture is a major concern when the keep-out zone (KOZ) and corresponding integration density of interconnect systems and transistor devices are considered. In this study, a finite element analysis (FEA)-based submodeling approach is demonstrated to analyze the stress-affected zone of through-silicon via (TSV) and its influences on a planar metal oxide semiconductor field transistor (MOSFET) device. The feasibility of the widely adopted analytical solution for TSV stress-affected zone estimation, Lamé radial stress solution, is investigated and compared with the FEA-based submodeling approach. Analytic results reveal that the Lamé stress solution overestimates the TSV-induced stress in the concerned device by over 50%, and the difference in the estimated results of device performance between Lamé stress solution and FEA simulation can reach 22%. Moreover, a silicon-germanium-based lattice mismatch stressor is designed in a silicon p-type MOSFET, and its effects are analyzed and compared with those of TSV residual stress. The S/D stressor dominates the stress status of the device channel. The demonstrated FEA-based submodeling approach is effective in analyzing the stress impact from packaging and device-level components and estimating the KOZ issue in advanced electronic packaging.

Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants.

Neutralizing antibodies (nAbs) elicited against the receptor binding site (RBS) of the spike protein of wild-type severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are generally less effective against recent variants of concern. RBS residues Glu484, Lys417, and Asn501 are mutated in variants first described in South Africa (B.1.351) and Brazil (P.1). We analyzed their effects on angiotensin-converting enzyme 2 binding, as well as the effects of two of these mutations (K417N and E484K) on nAbs isolated from COVID-19 patients. Binding and neutralization of the two most frequently elicited antibody families (IGHV3-53/3-66 and IGHV1-2), which can both bind the RBS in alternative binding modes, are abrogated by K417N, E484K, or both. These effects can be structurally explained by their extensive interactions with RBS nAbs. However, nAbs to the more conserved, cross-neutralizing CR3022 and S309 sites were largely unaffected. The results have implications for next-generation vaccines and antibody therapies.

Diverse immunoglobulin gene usage and convergent epitope targeting in neutralizing antibody responses to SARS-CoV-2.

It is unclear whether individuals with enormous diversity in B cell receptor repertoires are consistently able to mount effective antibody responses against SARS-CoV-2. We analyzed antibody responses in a cohort of 55 convalescent patients and isolated 54 potent neutralizing monoclonal antibodies (mAbs). While most of the mAbs target the angiotensin-converting enzyme 2 (ACE2) binding surface on the receptor binding domain (RBD) of SARS-CoV-2 spike protein, mAb 47D1 binds only to one side of the receptor binding surface on the RBD. Neutralization by 47D1 is achieved independent of interfering RBD-ACE2 binding. A crystal structure of the mAb-RBD complex shows that the IF motif at the tip of 47D1 CDR H2 interacts with a hydrophobic pocket in the RBD. Diverse immunoglobulin gene usage and convergent epitope targeting characterize neutralizing antibody responses to SARS-CoV-2, suggesting that vaccines that effectively present the receptor binding site on the RBD will likely elicit neutralizing antibody responses in a large fraction of the population.

Nanonetwork Thermosets from Templated Polymerization for Enhanced Energy Dissipation.

Herein, we aim to develop a facile method for the fabrication of mechanical metamaterials from templated polymerization of thermosets including phenolic and epoxy resins using self-assembled block copolymer, polystyrene-polydimethylsiloxane with tripod network (gyroid), and tetrapod network (diamond) structures, as templates. Nanoindentation studies on the nanonetwork thermosets fabricated reveal enhanced energy dissipation from intrinsic brittle thermosets due to the deliberate structuring; the calculated energy dissipation for gyroid phenolic resins is 0.23 nJ whereas the one with diamond structure gives a value of 0.33 nJ. Consistently, the gyroid-structured epoxy gives a high energy dissipation value of 0.57 nJ, and the one with diamond structure could reach 0.78 nJ. These enhanced properties are attributed to the isotropic periodicity of the nanonetwork texture with plastic deformation, and the higher number of struts in the tetrapod diamond network in contrast to tripod gyroid, as confirmed by the finite element analysis.

A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection.

Coronaviruses have caused several human epidemics and pandemics including the ongoing coronavirus disease 2019 (COVID-19). Prophylactic vaccines and therapeutic antibodies have already shown striking effectiveness against COVID-19. Nevertheless, concerns remain about antigenic drift in SARS-CoV-2 as well as threats from other sarbecoviruses. Cross-neutralizing antibodies to SARS-related viruses provide opportunities to address such concerns. Here, we report on crystal structures of a cross-neutralizing antibody, CV38-142, in complex with the receptor-binding domains from SARS-CoV-2 and SARS-CoV. Recognition of the N343 glycosylation site and water-mediated interactions facilitate cross-reactivity of CV38-142 to SARS-related viruses, allowing the antibody to accommodate antigenic variation in these viruses. CV38-142 synergizes with other cross-neutralizing antibodies, notably COVA1-16, to enhance neutralization of SARS-CoV and SARS-CoV-2, including circulating variants of concern B.1.1.7 and B.1.351. Overall, this study provides valuable information for vaccine and therapeutic design to address current and future antigenic drift in SARS-CoV-2 and to protect against zoonotic SARS-related coronaviruses.