Role of Non-local Interactions between CDR Loops in Binding Affinity of MR78 Antibody to Marburg Virus Glycoprotein

Cell-Based Platform for Antigen Testing and Its Application for SARS-CoV-2 Infection

We have engineered a cell that can be used for diagnosing active severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. Isolation of individuals with active infections offers an effective solution for mitigating pandemics. However, the implementation of this practice requires robust infrastructure for rapid and intuitive testing, which is currently missing in our communities. To address this need, we engineered a fast-growing cell line into a cell-based antigen test platform for emerging viruses, i.e., DxCell, that can be rapidly deployed in decentralized health care facilities for continuous testing. The technology was characterized using cells engineered to present spike glycoprotein of SARS-CoV-2 (SARS-CoV-2-Sgp-cells) and Calu-3 host cells infected with competent SARS-CoV-2. Preclinical validation was conducted by directly incubating the DxCell with oropharyngeal swabs from mice infected with SARS-CoV-2. No sample preparation steps are necessary. The DxCell quantitatively detected the SARS-CoV-2-Sgp-cells within 1 h (P < 0.02). Reporter signal was proportional to the number of SARS-CoV-2-Sgp-cells, which represents the infection burden. The SARS-CoV-2 DxCell antigen test was benchmarked against quantitative PCR (qPCR) test and accurately differentiated between infected (n = 8) and control samples (n = 3) (P < 0.05). To demonstrate the broad applicability of the platform, we successfully redirected its specificity and tested its sensing function with cells engineered to present antigens from other viruses. In conclusion, we have developed an antigen test platform that capitalizes on the two innate functions of the cell, self-replication and activation-induced cell signaling. These provide the DxCell key advantages over existing technologies, e.g., label-free testing without sample processing, and will facilitate its implementation in decentralized health care facilities.

IMPORTANCE Pandemic mitigation requires continuous testing of symptomatic or asymptomatic individuals with rapid turnaround time, and lack of this capability in our community has prolonged pandemic duration leading to obliteration of world economies. The DxCell platform is a cell-based self-replicative antigen test that detects molecular signatures of the target pathogen and can be distributed in small quantities to testing facilities for expansion on site to the desired volume. In this work, we directed this platform to target SARS-CoV-2. Unlike the PCR detection of viral mRNA that requires trained personnel, the DxCell does not require any sample preparation or signal amplification step and introduces an opportunity for a decentralized testing network.

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

Structure-based antibody and antigen design has advanced greatly in recent years, due not only to the increasing availability of experimentally determined structures but also to improved computational methods for both prediction and design. Constant improvements in performance within the Rosetta software suite for biomolecular modeling have given rise to a greater breadth of structure prediction, including docking and design application cases for antibody and antigen modeling. Here, we present an overview of current protocols for antibody and antigen modeling using Rosetta and exemplify those by detailed tutorials originally developed for a Rosetta workshop at Vanderbilt University. These tutorials cover antibody structure prediction, docking, and design and antigen design strategies, including the addition of glycans in Rosetta. We expect that these materials will allow novice users to apply Rosetta in their own projects for modeling antibodies and antigens.

Discovery of Marburg virus neutralizing antibodies from virus-naïve human antibody repertoires using large-scale structural predictions

Marburg virus (MARV) disease is lethal, with fatality rates up to 90%. Neutralizing antibodies (Abs) are promising drug candidates to prevent or treat the disease. Current efforts are focused in part on vaccine development to induce such MARV-neutralizing Abs. We analyzed the antibody repertoire from healthy unexposed and previously MARV-infected individuals to assess if naïve repertoires contain suitable precursor antibodies that could become neutralizing with a limited set of somatic mutations. We computationally searched the human Ab variable gene repertoire for predicted structural homologs of the neutralizing Ab MR78 that is specific to the receptor binding site (RBS) of MARV glycoprotein (GP). Eight Ab heavy-chain complementarity determining region 3 (HCDR3) loops from MARV-naïve individuals and one from a previously MARV-infected individual were selected for testing as HCDR3 loop chimeras on the MR78 Ab framework. Three of these chimerized antibodies bound to MARV GP. We then tested a full-length native Ab heavy chain encoding the same 17-residue-long HCDR3 loop that bound to the MARV GP the best among the chimeric Abs tested. Despite only 57% amino acid sequence identity, the Ab from a MARV-naïve donor recognized MARV GP and possessed neutralizing activity against the virus. Crystallization of both chimeric and full-length native heavy chain-containing Abs provided structural insights into the mechanism of binding for these types of Abs. Our work suggests that the MARV GP RBS is a promising candidate for epitope-focused vaccine design to induce neutralizing Abs against MARV.

Recent advances in marburgvirus research

Marburgviruses are closely related to ebolaviruses and cause a devastating disease in humans. In 2012, we published a comprehensive review of the first 45 years of research on marburgviruses and the disease they cause, ranging from molecular biology to ecology. Spurred in part by the deadly Ebola virus outbreak in West Africa in 2013-2016, research on all filoviruses has intensified. Not meant as an introduction to marburgviruses, this article instead provides a synopsis of recent progress in marburgvirus research with a particular focus on molecular biology, advances in animal modeling, and the use of Egyptian fruit bats in infection experiments.

A Comprehensive Analysis of Anion-Quadrupole Interactions in Protein Structures

The edgewise interactions of anions with phenylalanine (Phe) aromatic rings in proteins, known as anion-quadrupole interactions, have been well studied. However, the anion-quadrupole interactions of the tyrosine (Tyr) and tryptophan (Trp) rings have been less well studied, probably because these have been considered weaker than interactions of anions hydrogen bonded to Trp/Tyr side chains. Distinguishing such hydrogen bonding interactions, we comprehensively surveyed the edgewise interactions of certain anions (aspartate, glutamate, and phosphate) with Trp, Tyr, and Phe rings in high-resolution, nonredundant protein single chains and interfaces (protein-protein, DNA/RNA-protein, and membrane-protein). Trp/Tyr anion-quadrupole interactions are common, with Trp showing the highest propensity and average interaction energy for this type of interaction. The energy of an anion-quadrupole interaction (-15.0 to 0.0 kcal/mol, based on quantum mechanical calculations) depends not only on the interaction geometry but also on the ring atom. The phosphate anions at DNA/RNA-protein interfaces interact with aromatic residues with energies comparable to that of aspartate/glutamate anion-quadrupole interactions. At DNA-protein interfaces, the frequency of aromatic ring participation in anion-quadrupole interactions is comparable to that of positive charge participation in salt bridges, suggesting an underappreciated role for anion-quadrupole interactions at DNA-protein (or membrane-protein) interfaces. Although less frequent than salt bridges in single-chain proteins, we observed highly conserved anion-quadrupole interactions in the structures of remote homologues, and evolutionary covariance-based residue contact score predictions suggest that conserved anion-quadrupole interacting pairs, like salt bridges, contribute to polypeptide folding, stability, and recognition.