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At least 307 records · Page 17

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↗

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↗

A comparison of QTP functionals against coupled-cluster methods for EAs of small organic molecules

EA-EOM-CCSD electron affinities and LUMO energies of various Kohn–Sham density functional theory (DFT) methods are calculated for an a priori IP benchmark set of 64 small, closed-shell molecules. The purpose of these calculations was to investigate whether the QTP KS-DFT functionals can emulate EA-EOM-CC with only a mean-field approximation. We show that the accuracy of DFT—relative to CCSD—improves significantly when elements of correlated orbital theory are introduced into the parameterization to define the QTP family of functionals. In particular, QTP(02), which has only a single range separation parameter, provides results accurate to a MAD of <0.15 eV for the whole set of 64 molecules compared to EA-EOM-CCSD, far exceeding the results from the non-QTP family of density functionals.

Chemistry↗

Transferring a Molecular Foundation Model for Polymer Property Predictions

Transformer-based large language models have remarkable potential to accelerate design optimization for applications such as drug development and material discovery. Self-supervised pretraining of transformer models requires large-scale data sets, which are often sparsely populated in topical areas such as polymer science. Further, state-of-the-art approaches for polymers conduct data augmentation to generate additional samples but unavoidably incur extra computational costs. In contrast, large-scale open-source data sets are available for small molecules and provide a potential solution to data scarcity through transfer learning. In this work, we show that using transformers pretrained on small molecules and fine-tuned on polymer properties achieves comparable accuracy to those trained on augmented polymer data sets for a series of benchmark prediction tasks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A simple-structured benzo[1,2-b:4,5-b’]dithiophene-based molecule as a third component enables organic solar cells with over 18.2% efficiency

In this study, research has shown that ternary strategy is an effective tool for improving the performance of organic solar cells (OSCs) and simple-structured small molecules with low-cost and wide bandgap which broadens the scope of the choice in third components recently attracted the attention of researchers. Herein, a small molecule with benzo[1,2-b:4,5-b’]dithiophene (BDT) core named BR-C12 which mixed well with PM6 has been designed and synthesized. Incorporating BR-C12 as third component into PM6:Y6, BR-C12 exhibits a complementary absorption with PM6 and Y6, promoted exciton dissociation and charge collection, reduced bimolecular recombination, resulting in more ordered molecular packing. The PM6:Y6:BR-C12 (1:1.2:0.1, weight ratio) OSC shows an improved power conversion efficiency (PCE) of 17.02% in comparison to host binary devises (16.42%). In addition, by employing BR-C12 as third component into PM6:L8-BO, the ternary device based on PM6:L8-BO:BR-C12 also achieves significant enhancement in device photovoltaic performance with a PCE of 18.26%. In addition, BR-C12-added ternary devices exhibit improved stability than binary ones. This work presents a method for constructing high-performance ternary OSCs and enriches the abundance of materials for the third components.

14 SOLAR ENERGY↗

Chromatin activity precipitation method and system

Methods and systems for identifying binding sites in macromolecules using small molecule mimics of naturally occurring molecules is disclosed. A reactive probe is provided that mimics small molecule cofactors. A target macromolecule is irreversibly bound to the probe in vivo to selectively pull down or precipitate probe-bound macromolecules. The macromolecules may be, but are not limited to, DNA, RNA, and proteins.

59 BASIC BIOLOGICAL SCIENCES↗

High-dimensional isotomics, part 2: Observations of over 100 constraints on methionine's isotome

The abundances of different isotopic forms of a compound, or isotopologues, will vary based on its physical and chemical history. The number of isotopologues increases combinatorically with the size of a molecule, and even small molecules such as amino acids have thousands of potentially observable isotopic variants. However, due to the analytical challenges of separating and observing isotopologues, only a few dimensions of isotopic diversity are routinely measured. Overcoming these challenges requires both an experimental method to observe many isotopic properties and a theoretical framework for interpreting these experiments. In Part 1, we presented such a theoretical framework; here, we demonstrate an experimental method, which we apply to methionine. Our approach uses a Q Exactive HF Orbitrap to perform several “M + N experiments”, where a sample is ionized, a subset of its isotopologues with cardinal mass N daltons greater than the unsubstituted isotopologue is selected and fragmented, and the proportions of all detectable isotopic forms of those fragment ions are quantified. We perform M + 1, M + 2, M + 3, and M + 4 experiments of a methionine sample and standard where the sample has a 100 ‰ enrichment of 13C at the methyl carbon relative to the natural 13C abundance at that position in the standard, and is otherwise identical to the standard. We observe isotopic forms of 8 fragment ion species for each version of the M + N experiment. With the assistance of a forward model of expected mass spectra, we identify isotopic peaks for each fragment ion based on observed mass and abundance, screen these for data quality, and quantify abundances for 146 unique isotopic peaks at precisions of ≈ 0.3–3 ‰. We present our direct observations and use them to reconstruct the concentrations of 19 individual singly, doubly, and triply-substituted isotopologues; doing so gives fewer constraints and broader error bars than working with the direct observations, but may be more interpretable for some applications. We also examine possibilities for measuring additional peaks, which are primarily limited by the detection limit of the Orbitrap-IRMS method. We then suggest some possible uses of our direct measurements for chemical forensics and hypothesis testing. Furthermore, our results demonstrate the diversity of isotopic constraints currently observable and interpretable for organic molecules.

58 GEOSCIENCES↗

Rapid Computational Identification of Therapeutic Targets for Pathogens

Biological threats continue to persist and evolve as an important challenge to national security. There are multiple ways in which novel viral pathogens could emerge to pose a serious threat to human health. This project developed a pathogen target identification tool that can rapidly respond to a novel or emerging viral biological threat. A set of computational tools were developed that provide detailed information on the newly sequenced genes, their protein products and the drug target sites for the proteins that are best suited for biological countermeasure development. Three key innovations were developed in the project. 1) Development of a new extensive database of protein pocket structures with structure-based search algorithms to rapidly link novel protein targets with the complete collection of previously experimentally solved protein structures. 2) A novel clustering pipeline was introduced to group matching structures and associated small-molecule binding ligands into a consensus protein pocket with the associated small-molecule chemotypes predicted to fit in the pocket site. The matching experimentally solved structures were used to inform the value of different target sites. 3) Where there are viral protein targets with pockets structurally matched to similar human proteins, a biological knowledge graph, which links molecular interactions with human disease, was used to further assess the potential negative impact of a viral protein target with similarities to human proteins that could have important off target side effects. In total, the project produced a new resource for rapid and detailed assessment of promising targets for countermeasures, reflecting the ongoing wet lab, clinical, and computational data being collected. These capabilities will improve the ability to respond to a biological threat in multiple domains.

59 BASIC BIOLOGICAL SCIENCES↗

Solid-State Pathway Control via Reaction-Directing Heteroatoms: Ordered Pyridazine Nanothreads through Selective Cycloaddition

Nanothreads are one-dimensional nanomaterials comprised of a primarily sp 3 hydrocarbon backbone. They are typically formed through cycloaddition reactions induced by compression of small molecules to high pressures. Although nanothreads have been synthesized from a range of small molecule precursors (e.g., benzene, pyridine, aniline), the ability to control reaction pathways to produce atomically precise nanothreads with distinct chemical structures remains a difficult challenge. In this study, we show how heteroatoms incorporated within starting precursors can serve as “thread directing” groups by selecting for specific cycloaddition reaction pathways. By using a less-reactive diazine group within a six-membered aromatic ring, we successfully predict and synthesize the first carbon nanothread material derived from pyridazine (1,2-diazine, C 4 H 4 N 2 ). Compared with previous nanothreads, the synthesized polypyridazine, shows a predominantly uniform chemical structure with exceptional long-range order, allowing for structural characterization using vibrational spectroscopy and X-ray diffraction. The results demonstrate how thread-directing groups can be used for precise reaction pathway control and the formation of chemically precise nanothreads with a high degree of structural order.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Redox Mediators in Homogeneous Co-electrocatalysis

Homogeneous electrocatalysis has been well studied over the past several decades for the conversion of small molecules to useful products for green energy applications or as chemical feedstocks. However, in order for these catalyst systems to be used in industrial applications, their activity and stability must be improved. In naturally occurring enzymes, redox equivalents (electrons, often in a concerted manner with protons) are delivered to enzyme active sites by small molecules known as redox mediators (RMs). Inspired by this, co-electrocatalytic systems with homogeneous catalysts and RMs have been developed for the conversion of alcohols, nitrogen, unsaturated organic substrates, oxygen, and carbon dioxide. In these systems, the RMs have been shown to both increase the activity of the catalyst and shift selectivity to more desired products by altering catalytic cycles and/or avoiding high-energy intermediates. However, the area is currently underdeveloped and requires additional fundamental advancements in order to become a more general strategy. Furthermore, we summarize the recent examples of homogeneous co-electrocatalysis and discuss possible future directions for the field.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Activation of Hydrogen Under Ambient Conditions by Main Group Molecules

The major goals as indicated by the title are the detailed understanding of the interactions of main group compounds with small molecules such as H 2 , NH 3 , CO, C 2 H 4 and related species as well as the development of catalysts based on inexpensive main group (13 or 14) elements such as aluminum or silicon. A key feature of the compounds studied is the existence of Lewis acidic and basic sites at the main group element such that the small molecules become activated in a synergistic manner under relatively mild conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Do Molecular Fingerprints Identify Diverse Active Drugs in Large-Scale Virtual Screening? (No)

Computational approaches for small-molecule drug discovery now regularly scale to the consideration of libraries containing billions of candidate small molecules. One promising approach to increased the speed of evaluating billion-molecule libraries is to develop succinct representations of each molecule that enable the rapid identification of molecules with similar properties. Molecular fingerprints are thought to provide a mechanism for producing such representations. Here, we explore the utility of commonly used fingerprints in the context of predicting similar molecular activity. We show that fingerprint similarity provides little discriminative power between active and inactive molecules for a target protein based on a known active—while they may sometimes provide some enrichment for active molecules in a drug screen, a screened data set will still be dominated by inactive molecules. We also demonstrate that high-similarity actives appear to share a scaffold with the query active, meaning that they could more easily be identified by structural enumeration. Furthermore, even when limited to only active molecules, fingerprint similarity values do not correlate with compound potency. In sum, these results highlight the need for a new wave of molecular representations that will improve the capacity to detect biologically active molecules based on their similarity to other such molecules.

59 BASIC BIOLOGICAL SCIENCES↗

The role of transition metal formyl intermediates in the reduction of CO and CO 2

Transition-metal formyl (metalloformyl) complexes occupy a central position in the activation of small molecules, particularly in the reduction of carbon monoxide (CO) and carbon dioxide (CO 2 ). This review examines five decades of progress in the synthesis of metalloformyl complexes and investigations into their structure and reactivity. The bonding in the M–CHO unit is best described as a resonance hybrid between a classical σ-bound formyl ligand and an oxycarbene-like electronic structure, which governs their distinctive spectroscopic signatures and versatile reactivity. Established synthetic routes are summarized, including pathways involving hydride addition and CO insertion, alongside a discussion of the thermodynamic and kinetic factors that control formyl stability. Decomposition pathways and Lewis-acid stabilization strategies are analyzed as key design principles for extending metalloformyl lifetimes under catalytic conditions. Particular attention is given to hydride transfer processes and the role of metalloformyl intermediates as both reactive substrates and hydride sources in reduction chemistry. Lastly, emerging catalytic strategies that exploit metalloformyl intermediates in CO 2 and CO reduction are evaluated, highlighting how control of hydricity, redox potential, and secondary-sphere interactions enables selective C—H bond formation under comparatively mild conditions. Collectively, these studies establish metalloformyl complexes as mechanistically informative and functionally relevant intermediates that bridge fundamental organometallic chemistry with modern approaches to small-molecule activation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A High-Fidelity Molecular Model of the Cu(111) Repeating Unit

Dynamic processes at surfaces are central to heterogeneous catalysis, but their atomistic mechanism(s) can prove difficult to elucidate due to variations in material structure and the corresponding impact on reactivity. Moreover, disparities between reaction conditions and those employed for spectroscopic characterization at surfaces can inhibit detailed understanding of catalysis-relevant chemistries. Herein, we substantiate the so-called “cluster-surface” analogy by leveraging a low-valent tricopper architecture ( 1 ) as a model system for small molecule activation at Cu(111). Two reaction classes are explored: the adsorption of carbon monoxide (CO) and the dissociative adsorption of dihydrogen (H 2 ). These processes serve as an ideal testbed to compare the reactivity of a molecular cluster ( 1 ) to that of a heterogeneous surface, as both reactions have empirical data from measurements performed on crystalline Cu(111). Cluster 1 reversibly binds CO. Variable temperature NMR analysis with 13 CO reveals a favorable enthalpy but large negative entropy (−5.1 kcal × mol –1 and −22.9 cal × mol –1 × K –1 , respectively) for CO binding, affording a process that is marginally endergonic at room temperature (ΔG ads (298.15 K) = 1.7 ± 0.5 kcal × mol –1 ). Similarly, analogous to a Cu(111) surface, 1 is shown to oxidatively add (chemisorb) H 2 . Kinetic parameters were determined for this process and the activation enthalpy (8.4 ± 0.5 kcal × mol –1 ) closely mirrors that established for H 2 binding at the Cu(111) facet (6.0 to 12.4 kcal × mol –1 ). Together, these results showcase that a trinuclear cluster can reproduce the small molecule binding and activation energetics of a bulk crystalline surface, setting the stage for studying less-defined surface processes in an atomically precise molecular setting.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Kinetically Controlled Formation of Semi-crystalline Conjugated Polymer Nanostructures

Conjugated polymer (CP) materials that are considered as an attractive choice for various electronic and optoelectronic applications possess highly heterogeneous complex structures that can span several orders of magnitude in length scale. This is due to the intricate coupling effects of weak secondary interactions and entropic forces that determine molecular organization in bulk polymer materials. Understanding the influence of molecular interactions on the emergence and evolution of nano- and microscale structures is of paramount importance to the guided design and development of condensed CP materials. Such understanding is even more critical for the rational design of hierarchical systems away from equilibrium, where weak molecular interactions can guide the system along competing kinetic pathways toward local energy minima and metastable architectures. In this work, we studied a promising concept for accessing various kinetically stabilized semi-crystalline CP nanostructures that are formed in the process of controlled chain-growth Kumada catalyst-transfer polymerization initiated by a small-molecule catalytic species which can exist in equilibrium between free and aggregated states. Specifically, we chose a small-molecule perylenedicarboximide (PDCI) polymerization catalytic initiator which has a strong tendency toward reversible supramolecular assembly–disassembly that can be controlled by temperature. Addition of a thiophene monomer to a solution of the PDCI initiator starts the chain-growth polymerization process, which produces distinct nanoscale semi-crystalline polythiophene structures formed under predominant kinetic control. Furthermore, we demonstrated that, depending on the reaction temperature (which affects the fine balance between the position of PDCI assembly–disassembly equilibrium, rate of polymerization, and solvent–solute interactions for the growing polythiophene chains), a range of kinetically trapped hierarchically organized semi-crystalline CP systems with substantially varying optoelectronic properties could be obtained. In addition to spectroscopic and electron microscopic studies, in order to better reveal the structural aspects of the generated polymer nanoscale systems, we carried out a series of X-ray diffraction and neutron scattering experiments which indicated complex hierarchical organization in these kinetically stabilized CP assembled materials. We expect that this in situ polymerization-based approach can lead to a general way to expand access to various semi-crystalline CP nanostructured materials with broadly tunable electronic and optical properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High Energy Density Matter for Rocket Propulsion

The objective of the High Energy Density Matter (HEDM) program is to identify, develop, and exploit high energy atomic and molecular systems as energetic sources for rocket propulsion applications. It is a high risk, high payoff program that incorporates both basic and applied research, experimental and theoretical efforts, and science and engineering efforts. The HEDM program is co-sponsored by the Air Force Office of Scientific Research (AFOSR) and the Phillips Laboratory (PURKS). It includes both in-house and contracted University/Industry efforts. Technology developed by the HEDM program offers the opportunity for significant breakthroughs in propulsion system capabilities over the current state-of-the-art. One area of great interest is the use of cryogenic solids to increase the density of the propellant and to act as a stable matrix for storage of energetic materials. No cryogenic solid propellant has ever been used in a rocket, and there remain engineering challenges to such a propellant. However, these solids would enable a wide class of highly energetic materials by providing an environment that is at very low temperatures and is a physical barrier to recombination or energy loss reactions. Previous to our experiments only hydrogen atoms had been isolated in solid hydrogen. To date we have succeeded in trapping B, Al, Li, N, and Mg atoms in solid H2. Small molecules, such as B2 and LiB, are also of interest. Current efforts involve the search for new energetic small molecules, increasing free radical concentrations up to 5 mole percent, and scale-up for propulsion testing.

Carrick, Patrick G.↗

Revealing protonation states and tracking substrate in serine hydroxymethyltransferase with room-temperature X-ray and neutron crystallography

Pyridoxal 5’-phosphate (PLP)-dependent enzymes utilize a vitamin B 6 -derived cofactor to perform a myriad of chemical transformations on amino acids and other small molecules. Some PLP-dependent enzymes, such as serine hydroxymethyltransferase (SHMT), are promising drug targets for the design of small-molecule antimicrobials and anticancer therapeutics, while others have been used to synthesize pharmaceutical building blocks. Understanding PLP-dependent catalysis and the reaction specificity is crucial to advance structure-assisted drug design and enzyme engineering. Here we report the direct determination of the protonation states in the active site of Thermus thermophilus SHMT (TthSHMT) in the internal aldimine state using room-temperature joint X-ray/neutron crystallography. Conserved active site architecture of the model enzyme TthSHMT and of human mitochondrial SHMT (hSHMT2) were compared by obtaining a room-temperature X-ray structure of hSHMT2, suggesting identical protonation states in the human enzyme. The amino acid substrate serine pathway through the TthSHMT active site cavity was tracked, revealing the peripheral and cationic binding sites that correspond to the pre-Michaelis and pseudo-Michaelis complexes, respectively. At the peripheral binding site, the substrate is bound in the zwitterionic form. By analyzing the observed protonation states, Glu53, but not His residues, is proposed as the general base catalyst, orchestrating the retro-aldol transformation of L-serine into glycine.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Photo-Brook rearrangement of acyl silanes as a strategy for photoaffinity probe design

Photoaffinity labeling (PAL) is a powerful tool for the identification of non-covalent small molecule–protein interactions that are critical to drug discovery and medicinal chemistry, but this approach is limited to only a small subset of robust photocrosslinkers. The identification of new photoreactive motifs capable of covalent target capture is therefore highly desirable. Herein, we report the design, synthesis, and evaluation of a new class of PAL warheads based on the UV-triggered 1,2-photo-Brook rearrangement of acyl silanes, which hitherto have not been explored for PAL workflows. Irradiation of a series of probes in cell lysate revealed an iPr-substituted acyl silane with superior photolabeling and minimal thermal background labeling compared to other substituted acyl silanes. Further, small molecule (+)-JQ1- and rapamycin-derived iPr acyl silanes were shown to selectively label recombinant BRD4-BD1 and FKBP12, respectively, with minimal background. Together, these data highlight the untapped potential of acyl silanes as a novel, tunable scaffold for photoaffinity labeling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗