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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Significant Efficiency Enhancements in Non‐Y Series Acceptors by the Addition of Outer Side Chains

Abstract Most current highly efficient organic solar cells utilize small molecules like Y6 and its derivatives as electron acceptors in the photoactive layer. In this work, a small molecule acceptor, SC8‐IT4F, is developed through outer side chain engineering on the terminal thiophene of a conjugated 6,12‐dihydro‐dithienoindeno[2,3‐d:2′,3′‐d′]‐s‐indaceno[1,2‐b:5,6‐b′]dithiophene (IDTT) central core. Compared to the reference molecule C8‐IT4F, which lacks outer side chains, SC8‐IT4F displays notable differences in molecule geometry (as shown by simulations), thermal behavior, single‐crystal packing, and film morphology. Blend films of SC8‐IT4F and the polymer donor PM6 exhibit larger carrier mobilities, longer carrier lifetimes, and reduced recombination compared to C8‐IT4F, resulting in improved device performance. Binary photovoltaic devices based on the PM6:SC8‐IT4F films reveal an optimal efficiency over 15%, which is one of the best values for non‐Y type small molecule acceptors (SMAs). The resultant devices also show better thermal and operational stability than the control PM6:L8‐BO devices. SC8‐IT4F and its blend exhibit a higher relative degree of crystallinity and π coherence length, compared to C8‐IT4F samples, beneficial for charge transport and device performance. The results indicate that outer side chain engineering on existing small electron acceptors can be a promising molecular design strategy for further pursuing high‐performance organic solar cells.

He, Qiao [Department of Chemistry and Centre for P↗
DOE OSTI2025

ToF-SIMS spectral data analysis of Paenibacillus sp. 300A biofilms and planktonic cells

Analysis of bacterial biofilms is particularly challenging and important with diverse applications from systems biology to biotechnology. Among the variety of techniques that have been applied, time-of-flight secondary ion mass spectrometry (ToF-SIMS) has many promising features in studying the surface characteristics of biofilms. ToF-SIMS offers high spatial resolution and high mass accuracy, which permit surface sensitive analysis of biofilm components. Thus, ToF-SIMS provides a powerful solution to addressing the challenge of bacterial biofilm analysis. This dataset covers ToF-SIMS analysis of Paenibacillus sp. 300A (300A) isolated from the Hanford site in Richland, WA. The strain is known to have metal and sulfur reducing properties and can be used for bioremediation, wastewater treatment, bioengineering and technology development. There is a current need to identify small molecules and fragments produced from bacterial biofilms. Static ToF-SIMS spectra of 300A were obtained using an IONTOF TOF-SIMS V instrument equipped with a 25 keV Bi 3 + metal ion gun. Identified molecules and molecular fragments are compared against known biological databases and the reported peaks have at least 65 ppm mass accuracy. These molecules range from lipids and fatty acids to flavonoids, quinolones, and other naturally occurring organic compounds. It is anticipated that the spectral identification of key peaks will assist detection of metabolites, extracellular polymeric substance molecules like polysaccharides, and biologically relevant small molecules using ToF-SIMS in future surface and interface research of bacterial biofilms.

Biofilms↗
DOE OSTI2020

Selective inhibition of human translation termination by a drug-like compound

Methods to directly inhibit gene expression using small molecules hold promise for the development of new therapeutics targeting proteins that have evaded previous attempts at drug discovery. Among these, small molecules including the drug-like compound PF-06446846 (PF846) selectively inhibit the synthesis of specific proteins, by stalling translation elongation. These molecules also inhibit translation termination by an unknown mechanism. Using cryo-electron microscopy (cryo-EM) and biochemical approaches, we show that PF846 inhibits translation termination by arresting the nascent chain (NC) in the ribosome exit tunnel. The arrested NC adopts a compact α-helical conformation that induces 28 S rRNA nucleotide rearrangements that suppress the peptidyl transferase center (PTC) catalytic activity stimulated by eukaryotic release factor 1 (eRF1). These data support a mechanism of action for a small molecule targeting translation that suppresses peptidyl-tRNA hydrolysis promoted by eRF1, revealing principles of eukaryotic translation termination and laying the foundation for new therapeutic strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Quantum Chemistry Calculations for Metabolomics

A primary goal of metabolomics and exposomics studies is to fully characterize the small molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversi-ty present within the metabolome and exposome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials (“standards”), which are not available for most molecules. Computational quantum chemis-try methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alter-native route for building reference libraries, i.e., in silico libraries for “standards-free” identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solu-tion. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectros-copy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics and exposomics studies. We expect this review will inspire researchers in the field of small molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.

Metabolism↗
DOE OSTI2020

Crystalline Loading of Lipophilic Coenzyme Q10 Pharmaceuticals within Conjugated Carbon Aerogel Derivatives

Low-density aerogel materials currently are being considered for applications in controlling the rate of release for small-molecule pharmaceuticals in vivo. In particular, silica (SiO2) aerogels are an intriguing platform for controlling both the absolute amount of drug loading, but also the crystalline state of small molecule pharmaceuticals has been shown to affect drug release kinetics. To date, loading silica aerogel materials with crystalline pharmaceuticals typically require dissolving small molecules in a supercritical solvent (i.e., CO2) before drying to recover the aerogel/drug composite. Here we demonstrate a simple and low-cost method for controlling the crystallinity of the model drug coenzyme Q10 (CoQ10) within carbon aerogel materials by rationally controlling the chemical microstructure of the aerogel to exhibit ?-conjugated (sp2) chemical bonding. In particular, both pyrolyzed graphene and nanodiamond aerogels exhibit enhanced intrinsic drug loading capacity and CoQ10 crystallinity over a broad range of sp2 surface-curvature. In contrast, amorphous carbon aerogel materials are observed to load CoQ10 pharmaceuticals with strictly amorphous microstructure.

Lim, Mathew↗
NASA NTRS1994

Hydrophobic Porous Material Adsorbs Small Organic Molecules

Composite molecular-sieve material has pore structure designed specifically for preferential adsorption of organic molecules for sizes ranging from 3 to 6 angstrom. Design based on principle that contaminant molecules become strongly bound to surface of adsorbent when size of contaminant molecules is nearly same as that of pores in adsorbent. Material used to remove small organic contaminant molecules from vacuum systems or from enclosed gaseous environments like closed-loop life-support systems.

Sharma, Pramod K.↗
DOE OSTI2025

Conformational flexibility is a critical factor in designing broad-spectrum human norovirus protease inhibitors

Human norovirus (HuNoV) is a leading cause of gastroenteritis worldwide and is associated with significant morbidity, mortality, and economic impact. There are currently no licensed antiviral drugs for the treatment of HuNoV-associated gastroenteritis. The HuNoV protease plays a critical role in the initiation of virus replication by cleaving the polyprotein. Thus, it is an ideal target for developing antiviral small-molecule inhibitors. While rupintrivir, a potent small-molecule inhibitor of several picornavirus proteases, effectively inhibits GI.1 protease, it is an order of magnitude less effective against GII protease. Other GI.1 protease inhibitors also tend to be less effective against GII proteases. To understand the structural basis for the potency difference, we determined the crystal structures of proteases of GI.1, pandemic GII.4 (Houston and Sydney), and GII.3 in complex with rupintrivir. These structures show that the open substrate pocket in GI protease binds rupintrivir without requiring significant conformational changes, whereas, in GII proteases, the closed pocket flexibly extends, reorienting arginine-112 in the BII-CII loop to accommodate rupintrivir. Structures of R112A protease mutants with rupintrivir, coupled with enzymatic and inhibition studies, suggest R112 is involved in displacing both substrate and ligands from the active site, implying a role in the release of cleaved products during polyprotein processing. Thus, the primary determinant for differential inhibitor potency between the GI and GII proteases is the increased flexibility in the BII-CII loop of the GII proteases caused by the H-G mutation in this loop. Therefore, the inherent flexibility of the BII-CII loop in GII proteases is a critical factor to consider when developing broad-spectrum inhibitors for HuNoV proteases.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

RetroTide v1.0

RetroTide is a retrobiosynthesis software tool, designed to guide the design of biological pathways to make valuable small molecules. It takes as input a desired small molecule chemical structure, and outputs a design for a polyketide synthase enzyme (PKS) that has the closest possible chemical structure, as accessible by PKS chemistry. It is developed as a Python software library, and internally performs a search of the PKS design space, while simulating the chemicals produced by each design.

Backman, Tyler↗
DOE OSTI2022

Benzimidazole Based Hole‐Transporting Materials for High‐performance Inverted Perovskite Solar Cells

Abstract Interfaces play a decisive role in perovskite solar cells’ power conversion efficiency and their long‐term durability. Small‐molecule hole‐transporting materials (HTMs) have grabbed enormous attention due to their structural flexibility, material properties, and stabilities, allowing for improved operational durability in perovskite photovoltaics. This study synthesizes and investigates a new class of benzimidazole‐based small molecules, named YJS001 and YJS003 , serving as the HTMs to enable high‐efficiency mixed‐cation mixed‐halide perovskite solar cells. The benzimidazole‐based materials are dopant‐free HTMs composed of donor and acceptor building blocks that are designed to engineer the energy level alignment near the HTM/perovskite interface. Mixed‐cation mixed‐halide perovskites can be grown uniformly on both HTMs with large crystalline grains. It is discovered that the donor‐rich YJS003 ‐based solar cell exhibits a high open‐circuit voltage of 1.09 V with a champion power conversion efficiency of over 20%. Power‐dependent current–voltage characteristics of the solar cells are analyzed, from which the high performance of YJS003's excellent hole mobility and well‐aligned energy level is attributed. This work introduces a new class of benzimidazole‐based small molecules as HTMs, that paves the path for dopant free interface material development for commercialization of perovskite solar cells.

14 SOLAR ENERGY↗
DOE OSTI2021

Self-assembly of aramid amphiphiles into ultra-stable nanoribbons and aligned nanoribbon threads

Small molecule self-assembly is an established route for producing high surface area nanostructures with readily customizable chemistries and precise molecular organization. However, these structures are fragile, exhibiting molecular exchange, migration, and rearrangement - among other dynamic instabilities - and ultimately disassociate upon drying. Here we show a small molecule platform, the aramid amphiphile (AA), that overcomes these dynamic instabilities by incorporating a Kevlar-inspired domain into the molecular structure. Strong, anisotropic interactions between AAs suppress molecular exchange and elicit spontaneous self-assembly in water to form nanoribbons with lengths of up to 20 microns. The nanoribbons have a Young’s modulus of 1.7 GPa and tensile strength of 1.9 GPa. Here, we exploit this stability to extend small molecule self-assembly to hierarchically ordered macroscopic materials outside of solvated environments. Through an aqueous shear alignment process, we organize AA nanoribbons into arbitrarily long flexible threads that support 200 times their weight when dried. Tensile tests of the threads provide a benchmark for Young’s moduli (between ~400 and 600 MPa) and extensibilities (between ~0.6 and 1.1%) that depend on the counterion chemistry in solution. This bottom-up approach to macroscopic materials could benefit solid-state applications, historically inaccessible by self-assembled nanomaterials.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Inhibition of the C1s Protease and the Classical Complement Pathway by 6-(4-Phenylpiperazin-1-yl)Pyridine-3-Carboximidamide and Chemical Analogs

Abstract The classical pathway (CP) is a potent mechanism for initiating complement activity and is a driver of pathology in many complement-mediated diseases. The CP is initiated via activation of complement component C1, which consists of the pattern recognition molecule C1q bound to a tetrameric assembly of proteases C1r and C1s. Enzymatically active C1s provides the catalytic basis for cleavage of the downstream CP components, C4 and C2, and is therefore an attractive target for therapeutic intervention in CP-driven diseases. Although an anti-C1s mAb has been Food and Drug Administration approved, identifying small-molecule C1s inhibitors remains a priority. In this study, we describe 6-(4-phenylpiperazin-1-yl)pyridine-3-carboximidamide (A1) as a selective, competitive inhibitor of C1s. A1 was identified through a virtual screen for small molecules that interact with the C1s substrate recognition site. Subsequent functional studies revealed that A1 dose-dependently inhibits CP activation by heparin-induced immune complexes, CP-driven lysis of Ab-sensitized sheep erythrocytes, CP activation in a pathway-specific ELISA, and cleavage of C2 by C1s. Biochemical experiments demonstrated that A1 binds directly to C1s with a K d of ∼9.8 μM and competitively inhibits its activity with an inhibition constant (K i) of ∼5.8 μM. A 1.8-Å-resolution crystal structure revealed the physical basis for C1s inhibition by A1 and provided information on the structure–activity relationship of the A1 scaffold, which was supported by evaluating a panel of A1 analogs. Taken together, our work identifies A1 as a new class of small-molecule C1s inhibitor and lays the foundation for development of increasingly potent and selective A1 analogs for both research and therapeutic purposes.

Immunology↗
NASA NTRS1993

Theoretical research program to study chemical reactions in AOTV bow shock tubes

The main focus was the development, implementation, and calibration of methods for performing molecular electronic structure calculations to high accuracy. These various methods were then applied to a number of chemical reactions and species of interest to NASA, notably in the area of combustion chemistry. Among the development work undertaken was a collaborative effort to develop a program to efficiently predict molecular structures and vibrational frequencies using energy derivatives. Another major development effort involved the design of new atomic basis sets for use in chemical studies: these sets were considerably more accurate than those previously in use. Much effort was also devoted to calibrating methods for computing accurate molecular wave functions, including the first reliable calibrations for realistic molecules using full CI results. A wide variety of application calculations were undertaken. One area of interest was the spectroscopy and thermochemistry of small molecules, including establishing small molecule binding energies to an accuracy rivaling, or even on occasion surpassing, the experiment. Such binding energies are essential input to modeling chemical reaction processes, such as combustion. Studies of large molecules and processes important in both hydrogen and hydrocarbon combustion chemistry were also carried out. Finally, some effort was devoted to the structure and spectroscopy of small metal clusters, with applications to materials science problems.

Taylor, Peter R.↗
DOE OSTI2023

malbacR: A Package for Standardized Implementation of Batch Correction Methods for Omics Data

Mass spectrometry is a powerful tool for identifying and analyzing small molecules, such as metabolites and lipids, in com-plex biological samples. Liquid chromatography and gas chromatography mass spectrometry studies quite commonly in-volve large numbers of samples, which can require significant time for sample preparation and analyses. To accommodate such studies, the samples are commonly split into batches. Inevitably, variations in sample handling, temperature fluctua-tion, imprecise timing, column degradation and other factors result in systematic errors or biases of the measured abundances between the batches. Numerous methods are available via R packages to assist with batch correction for small molecule om-ics data; however, since these methods were developed by different research teams, the algorithms are available in separate R packages, each with different data input and output formats. We introduce the malbacR package which consolidates eleven common batch effect correction methods for small molecule omics data into one place so users can easily implement and compare: pareto scaling, power scaling, range scaling, ComBat, EigenMS, NOMIS, RUV-random, QC-RLSC, WaveI-CA2.0, TIGER, and SERRF. The malbacR package standardizes data input and output formats across these batch correction methods. The package works in conjunction with the pmartR package, allowing users to seamlessly include batch effect cor-rection in a pmartR workflow without needing any additional data manipulation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Forced Crowding of Colloids by Thermophoresis and Convection in a Custom Liquid Clusius–Dickel Microdevice

Here, we report a study demonstrating that simultaneous induction of a steady-state convection current and temperature gradient in a confined geometry can be an effective way to force crowding of dissolved particulates. To investigate this thermogravitationally driven concentration of particles in-situ, we developed a micro-device capable of sustaining controlled transverse temperature gradients within a 5 cm long, 0.1 mm inner diameter capillary that allowed visualization of particle movement with standard optical microscopy. Experiments were conducted on two material systems representative of nano-scale small molecules and micro-scale particles. With the small molecules (aromatic dyes, 530-790 g/mol, 1-1.5 nm) thermophoretic and gravitational effects in the micro-device resulted in an asymmetrical 2x concentration change along the capillary height over 3 days. In contrast, the concentration change under similar conditions for 40-micron diameter latex colloids is 50-fold in 30 minutes. This dramatic difference in separation times is consistent with simulations and models of thermophoresis where the thermophoretic effect scales with particle size. Induced crowding of particulates leads to formation of accumulation and depletion zones in at the bottom and top of the capillary respectively. Both the concentration of dye molecules over time in the depletion zone and spatial distribution of colloids over the entire capillary length were found to be good fits to simple first-order exponential decay functions. Furthermore, these results suggest potential applications of thermogravitational separation in developing new functional materials via thermophoretic and convective effects.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Prospects and challenges for nitrogen-atom transfer catalysis

Incorporation of nitrogen-based functional groups can profoundly impact the chemical and physical properties of organic small molecules. One-step conversion of C–H bonds to C–N bonds via C–H amination promises to streamline the synthesis of nitrogen-containing compounds. In pursuit of this promise, nitrogen-group transfer (NGT) from metal nitrenes (i.e., ligand supported M–NR complexes) has been the focus of intense research and development. In contrast, potentially complementary nitrogen-atom transfer (NAT) chemistry, in which a terminal metal nitride (i.e., ligand-supported M–N complex) engages with a C–H bond, is undeveloped. While the earliest examples of stoichiometric NAT chemistry were reported 25 years ago, catalytic protocols are only now beginning to emerge. Furthermore, we summarize the current state-of-the-art in NAT chemistry and discuss opportunities and challenges for the development of NAT catalysis as a platform for incorporation of nitrogen into organic small molecules. Specifically, we 1) highlight the synthetic complementarity of NGT and NAT chemistry, 2) discuss critical aspects of nitride electronic structure that dictate the philicity of supported metal atom, 3) examine the characteristic reactivity of metal nitrides towards substrate functionalization reactions, and 4) present emerging strategies and remaining obstacles to harnessing NAT for selective, catalytic nitrogenation of unfunctionalized organic small molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Probing the Sustainable Reduction of CO 2 , N 2 and NO 3 to Fuels and Chemicals using Non-Traditional Porphyrinoid Catalysts

For the last several decades, numerous strategies have been proposed to be able to interconvert electricity and commodity fuels for transportation and other applications. Even as solar and wind energy become more widely available, these renewable energy sources are not always available where the population is most dense or during peak times of energy demand. One plausible solution to the issue of electricity storage and transport is to use electricity to drive the formation of high-energy compounds and chemical fuels. As a result, the electrochemical conversion of CO 2 into chemical fuels has received major attention as a multi-pronged approach for electricity coversion, storage, and transport. Similar strategies are also attractive for conversion of N 2 and NO x into value added compounds such as ammonia. Metalloporphyrin and metallocorrole complexes are comprised of aromatic tetrapyrrole scaffolds and have been extensively studied as homogeneous catalysts for critical catalytic processes like the electrochemical CO 2 reduction reaction (eCO 2 RR) to generate CO as feedstock for the Fischer–Tropsch process to generate a variety of hydrocarbons as chemical fuels. Despite their significance and impact, efficiently driving such catalytic reduction processes is challenging for multiple reasons. Such processes require multiple-electron transfer events, as opposed to single-electron redox chemistry that forms high-energy singly-reduced intermediates. In addition, these electron transfer events must be coupled to proton-transfer steps and avoid application of high overpotentials where proton (H + ) reduction to generate H 2 (as well as other side-reactions) can lower the selectivity and energy efficiency of the eCO 2 RR process. Certain Fe(III) aromatic tetrapyrroles (e.g., porphyrins and corroles) have been reported to overcome these challenges, but are often difficult to synthesize and modify, and have a tendency to support single-electron redox chemistry at the metal as opposed to multielectron redox involving the ligand and metal in concert. Other families of tetrapyrroles in which all four meso-carbons are reduced (i.e., sp 3 -hybridized) are also known in the literature. These non-aromatic tetrapyrroles are known as porphyrinogens and support multi-electron redox chemistry which has been elaborated by several groups, prompting researchers to consider whether these scaffolds may improve the kinetics and efficiencies of multi-electron steps attendant to activation of thermodynamically stable small-molecule substrates such as CO 2 , N 2 , NO 3 − , and NO 2 − . Although porphyrinogens support multi-electron redox properties, the four sp 3 -hybridized meso-carbons inherent to the tetrapyrrole core completely disrupt π-conjugation between pyrrolic units, which compromises the photochemical properties of porphyrinogens in comparison to that of traditional porphyrinoids. Moreover, the highly reducing nature of porphyrinogens predisposes these platforms to extreme air and water sensitivity. Accordingly, such metalated porphyrinogens are often pyrophoric and/or incompatible with many common organic solvents (CH 2 Cl 2 , CHCl 3 , CH 3 CN, EtOAc, etc.). Hence, reports of efficient small-molecule activation or catalysis supported by porphyrinogens have been limited. To overcome the instability of porphyrinogens while retaining the scaffold’s attractive multi-electron redox properties, we have directed attention to establishing less-well studied groups of non-aromatic tetrapyrroles (i.e., phlorins, biladienes, and isocorroles). These non-traditional tetrapyrroles each contain just a single sp 3 -hybridized meso-carbon, which ablates the platforms aromaticity but still provides an extended π-framework. In addition to developing innovative platforms that may be used to sustainably generate value-added chemicals, fuels, and ammonia via either photo- or electrocatalytic approaches our work also has significantly broadened our understanding of how to prepare and modulate the properties of non-aromatic tetrapyrroles for other applications. Our efforts entailed a synergistic partnership and active collaborations with Drs. David C. Grills and Mehmed Z. Ertem (both of Brookhaven National Lab) to better characterize isocorroles (and related non-aromatic tetrapyrroles) using a variety of advanced spectroscopic and theoretical methods. Our combined efforts have shown that the combination of properties that isocorroles (and related tetrapyrroles) provide results in good chemical stability paired with unique redox and photochemical characteristics that are not typically supported by simple and/or unadorned aromatic tetrapyrroles. Beside redox chemistry, the photochemistry of isocorroles and other non-aromatic tetrapyrroles containing one sp 3 -hybridized meso-carbon is also appealing due to their absorption in the long-visible to near-IR regions, which are essential for photocatalysis and related applications that benefit from direct excitation at these wavelengths. The results reported vastly improve our understanding of non-aromatic tetrapyrrole synthesis, properties and utility for activation of small molecule substrates such as O 2 and CO 2 in the presence of weak cationic organic acids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Drug discovery efforts at George Mason University

With over 39,000 students, and research expenditures in excess of $200 million, George Mason University (GMU) is the largest R1 (Carnegie Classification of very high research activity) university in Virginia. Mason scientists have been involved in the discovery and development of novel diagnostics and therapeutics in areas as diverse as infectious diseases and cancer. Below are highlights of the efforts being led by Mason researchers in the drug discovery arena. To enable targeted cellular delivery, and non-biomedical applications, Veneziano and colleagues have developed a synthesis strategy that enables the design of self-assembling DNA nanoparticles (DNA origami) with prescribed shape and size in the 10 to 100 nm range. The nanoparticles can be loaded with molecules of interest such as drugs, proteins and peptides, and are a promising new addition to the drug delivery platforms currently in use. The investigators also recently used the DNA origami nanoparticles to fine tune the spatial presentation of immunogens to study the impact on B cell activation. These studies are an important step towards the rational design of vaccines for a variety of infectious agents. To elucidate the parameters for optimizing the delivery efficiency of lipid nanoparticles (LNPs), Buschmann, Paige and colleagues have devised methods for predicting and experimentally validating the pKa of LNPs based on the structure of the ionizable lipids used to formulate the LNPs. These studies may pave the way for the development of new LNP delivery vehicles that have reduced systemic distribution and improved endosomal release of their cargo post administration. To better understand protein-protein interactions and identify potential drug targets that disrupt such interactions, Luchini and colleagues have developed a methodology that identifies contact points between proteins using small molecule dyes. The dye molecules noncovalently bind to the accessible surfaces of a protein complex with very high affinity, but are excluded from contact regions. When the complex is denatured and digested with trypsin, the exposed regions covered by the dye do not get cleaved by the enzyme, whereas the contact points are digested. The resulting fragments can then be identified using mass spectrometry. The data generated can serve as the basis for designing small molecules and peptides that can disrupt the formation of protein complexes involved in disease processes. For example, using peptides based on the interleukin 1 receptor accessory protein (IL-1RAcP), Luchini, Liotta, Paige and colleagues disrupted the formation of IL-1/IL-R/IL-1RAcP complex and demonstrated that the inhibition of complex formation reduced the inflammatory response to IL-1B. Working on the discovery of novel antimicrobial agents, Bishop, van Hoek and colleagues have discovered a number of antimicrobial peptides from reptiles and other species. DRGN-1, is a synthetic peptide based on a histone H1-derived peptide that they had identified from Komodo Dragon plasma. DRGN-1 was shown to disrupt bacterial biofilms and promote wound healing in an animal model. The peptide, along with others, is being developed and tested in preclinical studies. Other research by van Hoek and colleagues focuses on in silico antimicrobial peptide discovery, screening of small molecules for antibacterial properties, as well as assessment of diffusible signal factors (DFS) as future therapeutics. The above examples provide insight into the cutting-edge studies undertaken by GMU scientists to develop novel methodologies and platform technologies important to drug discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Blocking C-terminal processing of KRAS4b via a direct covalent attack on the CaaX-box cysteine

RAS is the most frequently mutated oncogene in cancer. RAS proteins show high sequence similarities in their G-domains but are significantly different in their C-terminal hypervariable regions (HVR). These regions interact with the cell membrane via lipid anchors that result from posttranslational modifications (PTM) of cysteine residues. KRAS4b is unique as it has only one cysteine that undergoes PTM, C185. Small molecule covalent modification of C185 would block any form of prenylation and subsequently inhibit attachment of KRAS4b to the cell membrane, blocking its biological activity. We translated this concept to the discovery and development of disulfide tethering screen hits into irreversible covalent modifiers of C185. These compounds inhibited proliferation of KRAS4b-driven mouse embryonic fibroblasts, but not cells driven by N-myristoylated KRAS4b that harbor a C185S mutation and are not dependent on C185 prenylation. Top–down proteomics was used to confirm target engagement in cells. These compounds bind in a pocket formed when the HVR folds back between helix 3 and 4 in the G-domain (HVR-α3-α4). This interaction can happen in the absence of small molecules as predicted by molecular dynamics simulations and is stabilized in the presence of C185 binders as confirmed by small-angle X-ray scattering and solution NMR. NOESY-HSQC, an NMR approach that measures internuclear distances of 6 Å or less, and structure analysis identified the critical residues and interactions that define the HVR-α3-α4 pocket. Further development of compounds that bind to this pocket could be the basis of a new approach to targeting KRAS cancers.

C185↗