Abstract: Introduced here is an approach to developing molecules and molecule groups via a simulated mutagenesis process that is performed as part of in silico experimentation. Due to its initiation of the simulation based on a known binding interface or predicted binding interface between two structures—whether biological or synthetic—with known sequences, the approach introduced here can accomplish linear iteration of sequences. This can be accomplished whether these sequences relate to proteins, biological amino acids, synthetic amino acids, biological nucleic acids, synthetic nucleic acids, unnatural variants thereof, or any other molecules with a three-dimensional (“3D”) structure to evaluate the thermodynamic binding and affinity of the interaction as individual nucleic acids, amino acids or individual units of a polymer are mutated one at a time.

Abstract: Methods and compositions for manufacturing large-scale quantities of conjugatable peptides/peptoids/polymers/nucleic acids and conjugatable proteins, as well as hybrid materials consisting of synthetic and unnatural amino acids, glycopeptides, proteoglycans, and other molecular modifications are disclosed, for a variety of purposes including rapid antidote and vaccine applications in biodefense, therapeutics, diagnostics, theranostics, thin films, multilayered assemblies, biofilms, sensors, drug delivery vehicles, gene delivery vehicles, gene editing vehicles, staged release compounds, and the like.

Abstract: Provided herein are certain compositions and methods for nanoparticle seed substrates for self-assimilable nanoparticles and methods for optimized design of the same.

Abstract: Provided are methods and compositions for delivering a nucleic acid, protein, and/or ribonucleoprotein payload to a cell. Also provided are delivery molecules that include a peptide targeting ligand conjugated to a protein or nucleic acid payload (e.g., an siRNA molecule), or conjugated to a charged polymer polypeptide domain (e.g., poly-arginine such as 9R or a poly-histidine such as 6H, and the like). The targeting ligand provides for (i) targeted binding to a cell surface protein, and (ii) engagement of a long endosomal recycling pathway. As such, when the targeting ligand engages the intended cell surface protein, the delivery molecule enters the cell (e.g., via endocytosis) but is preferentially directed away from the lysosomal degradation pathway.

Abstract: Disclosed are small peptides derived from the binding interface of each of SARS-CoV-2 spike protein and ACE2 receptor, compositions comprising the same, and prophylactic and therapeutic uses of the peptides and the compositions. Also disclosed is a novel protocol of identifying, designing, and modifying the small peptides based on computer simulation.