Small Molecule Analogues Research Articles

P70S6K as a Potential Anti-COVID-19 Target: Insights from Wet Bench and In Silico Studies.

The onset of SARS-CoV-2 infection in 2019 sparked a global COVID-19 pandemic. This infection is marked by a significant rise in both viral and host kinase activity. Our primary objective was to identify a pivotal host kinase essential for COVID-19 infection and the associated phenomenon of the cytokine storm, which may lead to long-term COVID-19 complications irrespective of viral genetic variations. To achieve this, our study tracked kinase phosphorylation dynamics in RAW264.7 macrophages following SPIKE transfection over time. Among the kinases surveyed, p70S6K (RPS6KB1) exhibited a 3.5-fold increase in phosphorylation at S418. This significant change prompted the selection of p70S6K for in silico investigation, utilizing its structure bound to M2698 (PDB: 7N93). M2698, an oral dual Akt/p70S6K inhibitor with an IC50 of 1.1 nM, exhibited psychosis side effects in phase I clinical trials, potentially linked to its interaction with Akt2. Our secondary objective was to discover a small-molecule analogue of M2698 that exhibits a distinct binding preference for p70S6K over Akt2 through computational modeling and analysis. The in silico part of our project began with validating the prediction accuracy of the docking algorithm, followed by an OCA analysis pinpointing specific atoms on M2698 that could be modified to enhance selectivity. Subsequently, our investigation led to the identification of an analog of M2698, designated as S34, that showed a superior docking score towards p70S6K compared to Akt2. To further assess the stability of S34 in its protein-ligand (PL) complexes with p70S6K and Akt2, MD simulations were conducted. These simulations suggest that S34, on average, forms two hydrogen bond interactions with p70S6K, whereas it only forms one hydrogen bond interaction with Akt2. This difference in hydrogen bond interactions likely contributed to the observed larger root mean square deviation (RMSD) of 0.3 nm in the S34-Akt2 complex, compared to 0.1 nm in the S34-p70S6K complex. Additionally, we calculated free binding energy to predict the strength of the binding interactions of S34 to p70S6K and Akt2, which showed ~2-fold favorable binding affinity of S34 in the p70S6K binding pocket compared to that in the Akt2 binding pocket. These observations may suggest that the S34-p70S6K complex is more stable than the S34-Akt2 complex. Our work focused on identifying a host kinase target and predicting the binding affinity of a novel small molecule to accelerate the development of effective treatments. The wet bench results specifically highlight p70S6K as a compelling anti-COVID-19 target. Meanwhile, our in silico investigations address the known off-target effects associated with M2698 by identifying a close analog called S34. In conclusion, this study presents novel and intriguing findings that could potentially lead to clinical applications with further investigations.

Second-Coordination-Sphere Effects Reveal Electronic Structure Differences between the Mitochondrial Amidoxime Reducing Component and Sulfite Oxidase.

A combination of X-ray absorption and low-temperature electronic absorption spectroscopies has been used to probe the geometric and electronic structures of the human mitochondrial amidoxime reducing component enzyme (hmARC1) in the oxidized Mo(VI) and reduced Mo(IV) forms. Extended X-ray absorption fine structure analysis revealed that oxidized enzyme possesses a 5-coordinate [MoO2(SCys)(PDT)]- (PDT = pyranopterin dithiolene) active site with a cysteine coordinated to Mo. A 5-coordinate geometry is retained in the reduced state, with the equatorial oxo being protonated. Low-temperature electronic absorption spectroscopy of hmARC1 reveals a spectrum for the oxidized enzyme that is significantly different from what has been reported for sulfite oxidase family enzymes. Time-dependent density functional theory computations on oxidized and reduced hmARC1, and a small molecule analogue for hmARC1ox, have been used to assist us in making detailed band assignments and developing a greater understanding of enzyme electronic structure contributions to reactivity. Our understanding of the hmARCred HOMO and the LUMO of the benzamidoxime substrate reveal a potential π-bonding interaction between these redox orbitals, with two-electron occupation of the substrate LUMO along the reaction coordinate activating the O-N bond for cleavage and promoting oxygen atom transfer to the Mo site.

Dual Kv7.2/3-TRPV1 modulators inhibit nociceptor hyperexcitability and alleviate pain without target-related side effects.

Persistent or chronic pain is the primary reason people seek medical care, yet current therapies are either limited in efficacy or cause intolerable side effects. Diverse mechanisms contribute to the basic phenomena of nociceptor hyperexcitability that initiates and maintains pain. Two prominent players in the modulation of nociceptor hyperexcitability are the transient receptor potential vanilloid type 1 (TRPV1) ligand-gated ion channel and the voltage-gated potassium channel, Kv7.2/3, that reciprocally regulate neuronal excitability. Across many drug development programs targeting either TRPV1 or Kv7.2/3, significant evidence has been accumulated to support these as highly relevant targets; however, side effects that are poorly separated from efficacy have limited the successful clinical translation of numerous Kv7.2/3 and TRPV1 drug development programs. We report here the pharmacological profile of 3 structurally related small molecule analogues that demonstrate a novel mechanism of action (MOA) of dual modulation of Kv7.2/3 and TRPV1. Specifically, these compounds simultaneously activate Kv7.2/3 and enable unexpected specific and potent inhibition of TRPV1. This in vitro potency translated to significant analgesia in vivo in several animal models of acute and chronic pain. Importantly, this specific MOA is not associated with any previously described Kv7.2/3 or TRPV1 class-specific side effects. We suggest that the therapeutic potential of this MOA is derived from the selective and specific targeting of a subpopulation of nociceptors found in rodents and humans. This efficacy and safety profile supports the advancement of dual TRPV1-Kv7.2/3 modulating compounds into preclinical and clinical development for the treatment of chronic pain.

Mechanochemically accelerated deconstruction of chemically recyclable plastics.

Plastics redesign for circularity has primarily focused on monomer chemistries enabling faster deconstruction rates concomitant with high monomer yields. Yet, during deconstruction, polymer chains interact with their reaction medium, which remains underexplored in polymer reactivity. Here, we show that, when plastics are deconstructed in reaction media that promote swelling, initial rates are accelerated by over sixfold beyond those in small-molecule analogs. This unexpected acceleration is primarily tied to mechanochemical activation of strained polymer chains; however, changes in the activity of water under polymer confinement and bond activation in solvent-separated ion pairs are also important. Together, deconstruction times can be shortened by seven times by codesigning plastics and their deconstruction processes.

Active Site Characterization of a Campylobacter jejuni Nitrate Reductase Variant Provides Insight into the Enzyme Mechanism.

Mo K-edge X-ray absorption spectroscopy (XAS) is used to probe the structure of wild-type Campylobacter jejuni nitrate reductase NapA and the C176A variant. The results of extended X-ray absorption fine structure (EXAFS) experiments on wt NapA support an oxidized Mo(VI) hexacoordinate active site coordinated by a single terminal oxo donor, four sulfur atoms from two separate pyranopterin dithiolene ligands, and an additional S atom from a conserved cysteine amino acid residue. We found no evidence of a terminal sulfido ligand in wt NapA. EXAFS analysis shows the C176A active site to be a 6-coordinate structure, and this is supported by EPR studies on C176A and small molecule analogs of Mo(V) enzyme forms. The SCys is replaced by a hydroxide or water ligand in C176A, and we find no evidence of a coordinated sulfhydryl (SH) ligand. Kinetic studies show that this variant has completely lost its catalytic activity toward nitrate. Taken together, the results support a critical role for the conserved C176 in catalysis and an oxygen atom transfer mechanism for the catalytic reduction of nitrate to nitrite that does not employ a terminal sulfido ligand in the catalytic cycle.

Polymeric Materials as a Promising Platform for Suppressing Protein Aggregation Process

Abstract: The idea of designing novel anti-amyloid therapeutic agents has generated a lot of scientific interest and the potential for treating a variety of human pathophysiologies, such as neurodegenerative and non-neuropathic diseases linked to amyloid protein aggregation. To address this, different small molecules, peptides, surfactants, nanomaterials, etc., have been thoroughly investigated to learn more about their antiamyloidogenic capabilities, offering a great deal of potential for them to show up as future anti-amyloidogenic agents. In contrast to existing smallmolecule analogues, polymers have been envisaged as promising anti-amyloid agents for treating these diseases because of their enthralling physicochemical features and simplicity of functionalisation. This review article emphasises the latest developments in the design of synthetic polymers such as amino acid-conjugated polymers, glycopolymers, zwitterionic polymers and so on reported in the last decade in modulating amyloid aggregation process. Additionally, the structural function and mechanism involved in modifying the aggregation process are highlighted in order to inspire the researchers even more and provide insight into this important field of study.

Abstract 5976: R9: A novel NuRD complex inhibitor for targeted therapy in triple negative breast cancer (TNBC)

Abstract Triple Negative Breast Cancer (TNBC) is a highly aggressive breast cancer subtype, disproportionately affecting young and African American populations. TNBC constitutes up to 15% of breast cancers that lack effective targeted therapy. The Nucleosome Remodeling and Deacetylase (NuRD) complex, a pivotal chromatin remodeling entity, plays a crucial role in cancer development and progression. Specifically, the NuRD complex associates with SALL4 in cancer cells, contributing to the silencing of tumor-suppressor genes like PTEN. In this study, we discover R9, a novel small-molecule nucleotide analog, a first-in-class NuRD inhibitor. Utilizing computational and cellular methods, R9 demonstrated selective engagement with RBBP4, a key NuRD complex subunit. Cellular target engagement technology has been utilized to verify direct interaction of R9 with NuRD complex as well as to guide medicinal chemistry efforts. Mass spectrometry thermal proteome profiling (TPP) affirmed RBBP4 as the primary target of R9 with minimal off-target effects. In vitro studies reveal R9 displaying robust toxicity in TNBC cells, while sparing normal tissue derived cells. Encouragingly, R9 effectively impeded TNBC tumors growth in mice without inducing toxicity. Mechanistically, we demonstrate R9 induces DNA damage in sensitive TNBC cells, and the sensitivity correlates to DNA damage-vulnerable cancer cells, indicating DNA damage is a major effector of NuRD complex inhibition in TNBCs. We further demonstrate that R9 induces DNA damage through a c-MYC dependent manner. Ongoing studies aim to elucidate key transcription factors involved in NuRD complex inhibition and the role of MYC and DNA damage in response to NuRD complex inhibition. This research positions R9 as a promising candidate for targeted therapy in TNBC, offering potential insights into the intricate molecular pathways involved in TNBC tumor progression. Citation Format: Kun Zhang, Sheeba Jacob, Mikhail Dozmorov, Ivan Babic, Elmar Nurmemmedov, Anthony C. Faber. R9: A novel NuRD complex inhibitor for targeted therapy in triple negative breast cancer (TNBC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5976.

Growing concerns about using hypoxia-inducible factor prolyl hydroxylase inhibitors for the treatment of renal anemia.

Hypoxia-inducible factor prolyl hydroxylase inhibitors (HIF-PHIs) have emerged as a novel therapeutic class for treating anemia in patients with chronic kidney disease. Small molecule analogs of α-ketoglutarate (AKG), an essential substrate for 2-oxoglutarate-dependent dioxygenases (2-OGDDs), including prolyl hydroxylase domain proteins (PHDs), inhibit PHDs pharmacologically and thereby prevent HIF degradation. HIF stabilization alleviates anemia through several stimulatory effects on erythropoiesis, but it also affects the expression of many anemia-unrelated genes whose protein products exert important functions in vivo. Therefore, the pleiotropic effects of HIF stabilization under normoxic conditions deserve to be examined in more detail. Specifically, we believe that particular attention should be given to epigenetic modifications among the various AKG-based metabolic systems that may be altered by HIF-PHIs. It is noteworthy that AKG has been reported to exert health-protective actions. AKG-based metabolic systems include enzymes associated with the tricarboxylic acid cycle and amino acid metabolism, as well as 2-OGDD-mediated processes, which play important roles in many biological reactions. In this review, we examine the multifaceted effects of HIF-PHIs, encompassing not only their on-target effect of HIF stabilization but also their off-target inhibitory effects on various AKG-based metabolic systems. Furthermore, we examine its potential relevance to cardiovascular complications, based on clinical and animal studies suggesting its involvement in vascular calcification, thrombogenesis and heart failure. In conclusion, although HIF-PHIs offer a promising avenue for anemia treatment in CKD patients, their broader impact on multiple biological systems raises substantial concerns. The intricate interplay between HIF stabilization, AKG competition and cardiovascular complications warrants extensive, long-term investigations to ensure the safety and usefulness of HIF-PHIs in clinical practice.

Bicyclo[2.2.0]hexene: A Multicyclic Mechanophore with Reactivity Diversified by External Forces.

Polymer mechanochemistry has been established as an enabling tool in accessing chemical reactivity and reaction pathways that are distinctive from their thermal counterparts. However, eliciting diversified reaction pathways by activating different constituent chemical bonds from the same mechanophore structure remains challenging. Here, we report the design of a bicyclo[2.2.0]hexene (BCH) mechanophore to leverage its structural simplicity and relatively low molecular symmetry to demonstrate this idea of multimodal activation. Upon changing the attachment points of pendant polymer chains, three different C-C bonds in bicyclo[2.2.0]hexene are specifically activated via externally applied force by sonication. Experimental characterization confirms that in different scenarios of polymer attachment, the regioisomers of BCH undergo different activation reactions, entailing retro-[2+2] cycloreversion, 1,3-allylic migration, and retro-4π ring-opening reactions, respectively. Control experiments with small-molecule analogues reveal that the observed diversified reactivity of BCH regioisomers is possible only with mechanical force. Theoretical studies further elucidate that the differences in the positions of substitution between regioisomers have a minimal impact on the potential energy surface of the parent BCH scaffold. The mechanochemical selectivity between different C-C bonds in each constitutional isomer is a result of selective and effective coupling of force to the aligned C-C bond in each case.

Reduction in creatine metabolites in macrophages exposed to small molecule analogues of the anti-inflammatory parasitic worm product ES-62.

ES-62, a protein secreted by Acanthocheilonema viteae, is anti-inflammatory by virtue of covalently attached phosphorylcholine (PC) residues and thus a library of drug-like small molecule analogues (SMAs) based on its PC moieties has been designed for therapeutic purposes. Two members, SMAs 11a and 12b, were previously found to suppress production of pro-inflammatory cytokines by mouse bone marrow-derived macrophages (BMMs) exposed to cytosine-phosphate-guanosine oligodeoxynucleotides (CpG), agonists for Toll-like receptor 9. In order to explore the mechanism of action underlying such activities, an untargeted mass spectrometry-based metabolomics screen was undertaken. Stimulation of BMMs with CpG produced significant metabolic changes relating to glycolysis and the TCA cycle but the SMAs had little impact on this. Also, the SMAs did not promote alterations in metabolites known to be associated with macrophage M1/M2 polarization. Rather, BMMs exposed to SMAs 11a or 12b prior to CpG treatment, or even alone, revealed downregulation of metabolites of creatine, a molecule whose major role is in the transport of high energy phosphate from the mitochondria to the cytosol. These data therefore provide insight into a possible mechanism of action of molecules with significant therapeutic potential that has not previously been described for parasitic worm products.

Minimization of the E. coli ribosome, aided and optimized by community science.

The ribosome is a ribonucleoprotein complex found in all domains of life. Its role is to catalyze protein synthesis, the messenger RNA (mRNA)-templated formation of amide bonds between α-amino acid monomers. Amide bond formation occurs within a highly conserved region of the large ribosomal subunit known as the peptidyl transferase center (PTC). Here we describe the step-wise design and characterization of mini-PTC 1.1, a 284-nucleotide RNA that recapitulates many essential features of the Escherichia coli PTC. Mini-PTC 1.1 folds into a PTC-like structure under physiological conditions, even in the absence of r-proteins, and engages small molecule analogs of A- and P-site tRNAs. The sequence of mini-PTC 1.1 differs from the wild type E. coli ribosome at 12 nucleotides that were installed by a cohort of citizen scientists using the on-line video game Eterna. These base changes improve both the secondary structure and tertiary folding of mini-PTC 1.1 as well as its ability to bind small molecule substrate analogs. Here, the combined input from Eterna citizen-scientists and RNA structural analysis provides a robust workflow for the design of a minimal PTC that recapitulates many features of an intact ribosome.

Quorum sensing inhibiting dihydropyrrol-2-ones embedded polymer/graphene oxide nanocomposite waterborne antimicrobial coatings.

With increasing antibiotic resistance and hospital acquired microbial infections, there has been a growing interest to explore alternate antimicrobial approaches. This is particularly challenging when aiming to protect surfaces over a large area to avoid contact mediated infection transmission. Quorum sensing (QS) inhibition has emerged as an alternate antimicrobial approach overcoming evolutionary stress driven resistance observed in antibiotic treatment. However, specific surface orientation requirements and limited work on delivery of small molecule QS inhibiting compounds have limited their widespread applicability certainly when it comes to coating large surfaces. Here, we report antimicrobial nanocomposite coatings overcoming the dependence on molecular orientation of QS inhibiting dihydropyrrol-2-ones (DHP) analogues and release small molecule analogues. In a systematic study, we developed poly(styrene-stat-n-butyl acrylate)/graphene oxide (GO)/DHP analogue nanocomposite antimicrobial coatings that can be easily applied to surfaces of any length scale and studied their efficacy against Staphylococcus aureus. The polymer nanocomposite was designed to undergo coating formation at ambient temperature. The antimicrobial coatings exhibited DHP dose dependent antimicrobial response both in the supernatant growth media with a ∼7-log10 reduction in cell growth and virtually a complete inhibition in cell adhesion on the surface in the best coating compared to controls. When compared, DHP-Br coatings outperformed other DHP analogues (-F and -Ph) both in limiting the cell growth in the media and cellular adhesion on the coating surface. This is the first example of nanocomposite coatings comprising QS inhibiting compounds, and their exceptional performance is expected to pave the way for further research in the field.

Modular synthesis of triphenylphosphine-derived cage ligands for rhodium-catalyzed hydroformylation applications.

Four new triphenylphosphine-derived cage ligands were modularly synthesized via dynamic imine chemistry (DIC), and their absolute structures were characterized by single crystal X-ray diffraction (SXRD), nuclear magnetic resonance (NMR) and high resolution mass spectroscopy (HRMS). In contrast to small-molecule analogues, cage ligands demonstrate superior activity and selectivity. The Rh/Cage-L2 catalyst exhibits remarkable performance with an aldehyde selectivity of 89%, accompanied by a TOF value of 2665 h-1 and an l/b ratio of 2.60, thereby showcasing leading activity, chemical selectivity, and regioselectivity in the realm of homogeneous catalysts that rely on triphenylphosphine ligands. The reason for the formation of a higher l/b ratio, with a 3.84 kJ mol-1 difference in the energy of the rate-determining step, has been explained through density functional theory (DFT) calculations. In addition, a Janus-type PPh3-Au complex has been discovered during the study of the coordination of cage ligands, offering partial corroboration for the single coordination mechanism of these cage ligands. The large steric hindrance effect of cage ligands is believed to play a pivotal role in the hydroformylation reaction. This work highlights the potential application of cage ligands and inspires future efforts in the search of highly selective and efficient organometallic catalysts.

Exploring the Potential of Fenamate NSAID Analogs for the Treatment of Alzheimer’s Disease

AbstractBackgroundAlzheimer’s disease (AD) is the most common form of dementia, and its prevalence continues to increase with absence of available interventions. Drug repurposing accelerates the drug discovery process as therapeutics with known safety and toxicology profiles are considered. Although the blood‐brain barrier (BBB) prevents uptake of most pharmaceuticals, our laboratory previously showed that tolfenamic acid (TA), a fenamate non‐steroidal anti‐inflammatory drug (NSAID) with known anti‐cancer effects, can cross the BBB and slow the progression of AD (Zawia et al, 2018).MethodIn the present study, we test 2‐(2‐Cyanophenylthio) benzoic acid (CBA) and Niflumic acid (NA), small molecule analogs of TA that showed better safety and efficacy at targeting neurodegenerative pathways in vitro, and a similar mechanism of action to TA. We aimed to examine the effects of the analogs on in mice using proteomic and transcriptomic analyses.Single dose study of TA, CBA, and NA was carried out in C57BL/6 mice following oral administration at 100 mg/kg. Differential expression of genes and proteomic biomarkers in mice cortices were analyzed between each treatment group and a corresponding control group.ResultsAnalysis of the number of perturbed genes revealed that the drugs demonstrate limited off‐target effects. Bioinformatic analyses revealed that the therapeutics targeted cancer and neurodegenerative pathways including autophagy, inflammation, and neuronal trafficking. CBA and NA shared common downstream targets and pathways suggesting that they may have a similar mode of action.ConclusionWe found a set of differentially expressed genes that have been linked to processes involved in AD pathogenesis such as the production and clearance of neurotoxic Aβ peptides, tau phosphorylation, regulation of oxidative stress, and inflammatory processes. These results suggest that the drugs may influence pathways related to the pathogenesis of AD and support the potential of drug repurposing of fenamate NSAIDs such as TA, and its analogs CBA and NA, as a strategy for cancer and neurodegenerative disease therapy. Further research is needed to confirm the effect of the analogs on AD biomarkers and their efficacy as therapeutics for AD.

Small molecule activators of TAK1 promotes its activity-dependent ubiquitination and TRAIL-mediated tumor cell death

TAK1 is a key modulator of both NF-κB signaling and RIPK1. In TNF signaling pathway, activation of TAK1 directly mediates the phosphorylation of IKK complex and RIPK1. In a search for small molecule activators of RIPK1-mediated necroptosis, we found R406/R788, two small molecule analogs that could promote sustained activation of TAK1. Treatment with R406 sensitized cells to TNF-mediated necroptosis and RIPK1-dependent apoptosis by promoting sustained RIPK1 activation. Using click chemistry and multiple biochemical binding assays, we showed that treatment with R406 promotes the activation of TAK1 by directly binding to TAK1, independent of its original target Syk kinase. Treatment with R406 promoted the ubiquitination of TAK1 and the interaction of activated TAK1 with ubiquitinated RIPK1. Finally, we showed that R406/R788 could promote the cancer-killing activities of TRAIL in vitro and in mouse models. Our studies demonstrate the possibility of developing small molecule TAK1 activators to potentiate the effect of TRAIL as anticancer therapies.

A water-soluble and biocompatible chitosan-based fluorescent probe for real-time monitoring formaldehyde in living cells and zebrafish

Formaldehyde (HCHO) is a common environmental toxicant that can harm the human respiratory tract and nervous system when exposed for long period of time. As a carcinogen, HCHO also increases the risk of cancer in humans. HCHO can be produced endogenously in living systems and plays an essential role in physiological and biochemical reactions and pathogenesis. Therefore, monitoring the level of HCHO in vivo and in vitro has become the focus of attention. The designed naphthalene fluorophore was introduced onto modified chitosan to prepare a chitosan-based fluorescent probe (CS-FA) for HCHO detection. Compared to other small-molecule probe analogs for the detection of HCHO, the randomly coiled polymer chain of chitosan enabled CS-FA to “enrich” HCHO using the synergistic binding of hydrazino-naphthalimide recognition sites. Thus, the reaction of the analyte with the recognition site was accelerated, resulting in a faster equilibrium fluorescence response (2–3 min) and high sensitivity. In addition, the introduction of biomass material chitosan also improved the biocompatibility of the probe. Then a series of composite materials (test strips and hydrogel) were prepared based on the probe to expand the application form of the probe.

Manipulation of plant immunity via an mRNA decapping pathogen effector.

This article is a Commentary on McCombe et al. (2023), 239: 222–239.

Epidemiology, symptoms, transmission, prevention, treatment, and future prospects of the Lassa fever outbreak: a potential study.

Epidemiology, symptoms, transmission, prevention, treatment, and future prospects of the Lassa fever outbreak: a potential study.

GAP positions catalytic H-Ras residue Q61 for GTP hydrolysis in molecular dynamics simulations, complicating chemical rescue of Ras deactivation

Functional interaction of Ras signaling proteins with upstream, negative regulatory GTPase activating proteins (GAPs) represents a crucial step in cellular decision making related to growth and survival. Key components of the catalytic transition state for Ras deactivation by GAP-accelerated hydrolysis of Ras-bound guanosine triphosphate (GTP) are thought to include an arginine residue from the GAP (the arginine finger), a glutamine residue from Ras (Q61), and a water molecule that is likely coordinated by Q61 to engage in nucleophilic attack on GTP. Here, we use in-vitro fluorescence experiments to show that 0.1–100 mM concentrations of free arginine, imidazole, and other small nitrogenous molecule fail to accelerate GTP hydrolysis, even in the presence of the catalytic domain of a mutant GAP lacking its arginine finger (R1276A NF1). This result is surprising given that imidazole can chemically rescue enzyme activity in arginine-to-alanine mutant protein tyrosine kinases (PTKs) that share many active site components with Ras/GAP complexes. Complementary all-atom molecular dynamics (MD) simulations reveal that an arginine finger GAP mutant still functions to enhance Ras Q61-GTP interaction, though less extensively than wild-type GAP. This increased Q61-GTP proximity may promote more frequent fluctuations into configurations that enable GTP hydrolysis as a component of the mechanism by which GAPs accelerate Ras deactivation in the face of arginine finger mutations. The failure of small molecule analogs of arginine to chemically rescue catalytic deactivation of Ras is consistent with the idea that the influence of the GAP goes beyond the simple provision of its arginine finger. However, the failure of chemical rescue in the presence of R1276A NF1 suggests that the GAPs arginine finger is either unsusceptible to rescue due to exquisite positioning or that it is involved in complex multivalent interactions. Therefore, in the context of oncogenic Ras proteins with mutations at codons 12 or 13 that inhibit arginine finger penetration toward GTP, drug-based chemical rescue of GTP hydrolysis may have bifunctional chemical/geometric requirements that are more difficult to satisfy than those that result from arginine-to-alanine mutations in other enzymes for which chemical rescue has been demonstrated.

STING antagonists, synthesized via Povarov-Doebner type multicomponent reaction.

The cGAS-STING axis plays an important role in protecting higher organisms against invading pathogens or cancer by promoting the production of cytokines and interferons. However, persistent or uncontrolled activation of this pathway could lead to inflamed environments, which is detrimental to the host in the long run. Persistent activation of STING is known to be the cause of STING-associated vasculopathy with onset in infancy (SAVI) and activated STING is believed to play important roles in worsening various diseased states, such as traumatic brain injury, diabetic kidney disease and colitis. Thus, antagonists of STING could play important roles in managing various inflammatory diseases. Herein, we report the discovery of small molecule STING inhibitors, HSD1077 and analogs, which are facilely synthesized via a Povarov-Doebner type three-component reaction involving an amine, ketone, and aldehyde. Structure-activity relationship, SAR, studies indicate that both the 3H-pyrazolo[4,3-f]quinoline and pyrazole moieties in HSD1077 are critical for STING binding. At concentrations as low as 20 nM, HSD1077 suppressed type-1 interferon expression in both murine RAW macrophages and human THP-1 monocytes upon treatment with 100 μM 2'-3' cGAMP. Compounds containing the 3H-pyrazolo[4,3-f]quinoline moiety have the potential to be translated into anti-inflammatory compounds via STING inhibition.