Multivalent Small-Molecule Pan-RAS Inhibitors.

Design of small molecules that disrupt protein-protein interactions, including the interaction of RAS proteins and their effectors, may provide chemical probes and therapeutic agents. We describe here the synthesis and testing of potential small-molecule pan-RAS ligands, which were designed to interact with adjacent sites on the surface of oncogenic KRAS. One compound, termed 3144, was found to bind to RAS proteins using microscale thermophoresis, nuclear magnetic resonance spectroscopy, and isothermal titration calorimetry and to exhibit lethality in cells partially dependent on expression of RAS proteins. This compound was metabolically stable in liver microsomes and displayed anti-tumor activity in xenograft mouse cancer models. These findings suggest that pan-RAS inhibition may be an effective therapeutic strategy for some cancers and that structure-based design of small molecules targeting multiple adjacent sites to create multivalent inhibitors may be effective for some proteins.

Protein folding drives disulfide formation.

PDI catalyzes the oxidative folding of disulfide-containing proteins. However, the sequence of reactions leading to a natively folded and oxidized protein remains unknown. Here we demonstrate a technique that enables independent measurements of disulfide formation and protein folding. We find that non-native disulfides are formed early in the folding pathway and can trigger misfolding. In contrast, a PDI domain favors native disulfides by catalyzing oxidation at a late stage of folding. We propose a model for cotranslational oxidative folding wherein PDI acts as a placeholder that is relieved by the pairing of cysteines caused by substrate folding. This general mechanism can explain how PDI catalyzes oxidative folding in a variety of structurally unrelated substrates.

Who Are the Local Policy Innovators? Cluster Analysis of Municipal Tobacco Control Policies in Massachusetts.

CONTEXT: Tobacco use is a leading cause of preventable death, yet it is challenging to establish public policy to reduce tobacco use. Massachusetts has been a national leader in tobacco control, and its policy-making patterns can be informative to the country. OBJECTIVE: To identify factors associated with the adoption of tobacco policy within 351 Massachusetts municipalities. DESIGN: We obtained the 2019 Massachusetts municipality-level tobacco control policy information from Massachusetts' Tobacco Automated Fact Sheet Information system and compiled it with data from American Community Survey, Massachusetts Municipal Association, and Massachusetts state government's Web sites. We used k -means clustering method to identify statistical clustering patterns and hotspot analysis (Getis-Ord Gi*) and Local Indicators of Spatial Association to identify geographic clustering patterns. We then performed multinomial logistic regression to identify factors associated with policy clusters. SETTING: Massachusetts. PARTICIPANTS: Three hundred fifty-one municipalities in Massachusetts. MAIN OUTCOME MEASURE: Policy clusters-groups of municipalities with similar tobacco control policy behaviors. RESULTS: Based on the k -means analyses, we identified 3 clusters in Massachusetts municipal tobacco control policy behaviors: 54% (N = 191) of municipalities were "Policy Leaders" with a high adoption rate of the 6 tobacco control policies; 18% (N = 63) were "Peer-Influenced Actors" focused on tobacco purchase restrictions for individuals younger than 21 years; and 28% (N = 97) were "Policy Non-Actors," with no tobacco control policies in place. Policy Leaders were geographically clustered in larger cities and the MetroWest region. Policy Non-Actors were clustered in rural areas of Western and Central Massachusetts. Larger municipal population size, higher municipal tax income, and higher percentages of residents voting Democratic were associated with higher policy adoption activities. CONCLUSIONS: Local variation in the adoption of tobacco policies may exacerbate inequities in tobacco use and population health. Opportunities remain to implement additional tobacco control regulations at the local level to promote public health.

Non-Surgical Correction of Congenital Ear Anomalies: A Critical Assessment of Caretaker Burdens and Aesthetic Outcomes.

INTRODUCTION: Congenital ear anomalies result from cartilage and skin compression in utero. They can be corrected in infancy before the cartilage hardens and loses its malleability. Caretaker burden of ear molding and its impact on esthetic outcomes has not been studied. METHODS: Demographic and procedural variables were retrospectively collected for infants who underwent ear molding. Parents were surveyed regarding their experience, caretaker burden, and esthetic outcome. Outside physicians were provided with pre- and post-treatment photographs and asked to rate outcomes. A Likert scale was developed for responses and converted to a numeric score from 1 to 5 with 5 as the most desirable. RESULTS: Seventy-four patients comprising 121 ears were included. Mean age at treatment was 20.1 ± 21.4 days with treatment duration of 21.1 ± 7.7 days. Parental participation in the survey was 70.1%. Questions that queried parents' experiences revealed a "very positive" experience with minor burden related to bathing and cleaning (Mean Likert Score 4.1, Range 1-5). Favorable parent-reported outcomes were obtained regarding anticipated social distress (4.28, 1-5), satisfaction with results (4.27, 1-5), and perception of final appearance (4.18, 1-5). Physician assessments of esthetic outcomes were slightly lower, but favorable between "somewhat effective" and "very effective" (3.46, 1-5). Earlier treatment trended favorably, but did not reach significance. Ear malformations had higher parent-reported satisfaction than ear deformations (4.75 ± 0.46 vs 4.21 ± 1.25, p = 0.025). CONCLUSION: Despite the additional obligation for new parents, infant ear molding is rated low in terms of caretaker burden. Esthetic outcomes are excellent as assessed by parents and physicians. However, caretakers reported higher esthetic outcomes than physician evaluations. LEVEL OF EVIDENCE IV: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266.

Building trans-bicyclo[4.4.0]decanes/decenes in complex multifunctional frameworks: the case for antibiotic development.

Covering: 2000 to 2020. trans-Bicyclo[4.4.0]decane/decene (such as trans-decalin and trans-octalin)-containing natural products display a wide range of structural diversity and frequently exhibit potent and selective antibacterial activities. With one of the major factors in combatting antibiotic resistance being the discovery of novel scaffolds, the efficient construction of these natural products is an attractive pursuit in the development of novel antibiotics. This highlight aims to provide a critical analysis on how the presence of dense architectural and stereochemical complexity necessitated special strategies in the synthetic pursuits of these natural trans-bicyclo[4.4.0]decane/decene antibiotics.

Promiscuous Pseudomonas: Uptake of Non-Endogenous Ligands for Iron Acquisition.

Iron is an essential nutrient to nearly all living beings. However, its acquisition poses a significant challenge to many organisms, including most bacteria. One of the main iron uptake strategies employed by bacteria is the uptake of siderophores, small molecules that chelate extracellular iron. The pathogenic species Pseudomonas aeruginosa produces two different siderophores, pyochelin and pyoverdine. P. aeruginosa senses the amount of bioavailable extracellular iron in order to regulate the production levels of each of these two siderophores. In previous work, we found that a series of pyochelin biosynthetic shunt products enhanced the growth of P. aeruginosa in iron-depleted conditions when prechelated with iron. Thus, on the basis of these results, we investigated the physiochemical and biological properties of a series of non-native oxygen counterparts to these metabolites in the current study.

Small molecule modulator of protein disulfide isomerase attenuates mutant huntingtin toxicity and inhibits endoplasmic reticulum stress in a mouse model of Huntington's disease.

Huntington's disease (HD) is caused by a cytosine-adenine-guanine (CAG) trinucleotide repeat expansion in the huntingtin (HTT) gene encoding an elongated polyglutamine tract within the N-terminal of the huntingtin protein (Htt) and leads to Htt misfolding, aberrant protein aggregation, and progressive appearance of disease symptoms. Chronic activation of endoplasmic reticulum (ER) stress by mutant Htt (mHtt) results in cellular dysfunction and ultimately cell death. Protein disulfide isomerase (PDI) is a chaperone protein located in the ER. Our previous studies demonstrated that mHtt caused PDI to accumulate at mitochondria-associated ER membranes and triggered cell death, and that modulating PDI activity using small molecules protected cells again mHtt toxicity in cell and brain slice models of HD. In this study, we demonstrated that PDI is upregulated in the HD human brain, in cell and mouse models. Chronic administration of a reversible, brain penetrable small molecule PDI modulator, LOC14 (20 mg/kg/day), significantly improved motor function, attenuated brain atrophy and extended survival in the N171-82Q HD mice. Moreover, LOC14 preserved medium spiny neuronal marker dopamine- and cyclic-AMP-regulated phosphoprotein of molecular weight 32 000 (DARPP32) levels in the striatum of HD mice. Mechanistic study revealed that LOC14 suppressed mHtt-induced ER stress, indicated by repressing the abnormally upregulated ER stress proteins in HD models. These findings suggest that LOC14 is promising to be further optimized for clinical trials of HD, and modulation of signaling pathways coping with ER stress may constitute an attractive approach to reduce mHtt toxicity and identify new therapeutic targets for treatment of HD.

Ligand binding to a remote site thermodynamically corrects the F508del mutation in the human cystic fibrosis transmembrane conductance regulator.

Many disease-causing mutations impair protein stability. Here, we explore a thermodynamic strategy to correct the disease-causing F508del mutation in the human cystic fibrosis transmembrane conductance regulator (hCFTR). F508del destabilizes nucleotide-binding domain 1 (hNBD1) in hCFTR relative to an aggregation-prone intermediate. We developed a fluorescence self-quenching assay for compounds that prevent aggregation of hNBD1 by stabilizing its native conformation. Unexpectedly, we found that dTTP and nucleotide analogs with exocyclic methyl groups bind to hNBD1 more strongly than ATP and preserve electrophysiological function of full-length F508del-hCFTR channels at temperatures up to 37 °C. Furthermore, nucleotides that increase open-channel probability, which reflects stabilization of an interdomain interface to hNBD1, thermally protect full-length F508del-hCFTR even when they do not stabilize isolated hNBD1. Therefore, stabilization of hNBD1 itself or of one of its interdomain interfaces by a small molecule indirectly offsets the destabilizing effect of the F508del mutation on full-length hCFTR. These results indicate that high-affinity binding of a small molecule to a remote site can correct a disease-causing mutation. We propose that the strategies described here should be applicable to identifying small molecules to help manage other human diseases caused by mutations that destabilize native protein conformation.

Proteomics insights into infantile neuronal ceroid lipofuscinosis (CLN1) point to the involvement of cilia pathology in the disease.

Mutations in the depalmitoylation enzyme, palmitoyl protein thioesterase (PPT1), result in the early onset neurodegenerative disease known as Infantile Neuronal Ceroid Lipofuscinosis. Here, we provide proteomic evidence suggesting that PPT1 deficiency could be considered as a ciliopathy. Analysis of membrane proteins from brain enriched for acylated proteins from neonate Ppt1 knock out and control mice revealed a list of 88 proteins with differential expression levels. Amongst them, we identified Rab3IP, which regulates ciliogenesis in concert with Rab8 and Rab11. Immunostaining analysis revealed that PPT1 is localized in the cilia. Indeed, an unbiased proteomics analysis on isolated cilia revealed 660 proteins, which differed in their abundance levels between wild type and Ppt1 knock out. We demonstrate here that Rab3IP, Rab8 and Rab11 are palmitoylated, and that palmitoylation of Rab11 is required for correct intracellular localization. Cells and brain preparations from Ppt1-/- mice exhibited fewer cells with cilia and abnormally longer cilia, with both acetylated tubulin and Rab3IP wrongly distributed along the length of cilia. Most importantly, the analysis revealed a difference in the distribution and levels of the modified proteins in cilia in the retina of mutant mice versus the wildtype, which may be important in the early neurodegenerative phenotype. Overall, our results suggest a novel link between palmitoylated proteins, cilial organization and the pathophysiology of Neuronal Ceroid Lipofuscinosis.

From General to Specific: Can Pseudomonas Primary Metabolism Be Exploited for Narrow-Spectrum Antibiotics?

The spread of antimicrobial resistance is a major threat to human health, and patients requiring prolonged antibiotic exposure are in desperate need of new therapeutic strategies. It has been hypothesized that tailoring our antibiotics to inhibit molecular targets specific to pathogens might stem the spread of resistance. A prime candidate for such a strategy is Pseudomonas aeruginosa, which can be found in the lungs of nearly all adult cystic fibrosis patients and, due to chronic exposure to antibiotics, has a high rate of multidrug-resistant strains. Although much research has been done on P. aeruginosa virulence factors as narrow-spectrum targets, less attention has been paid to primary carbon metabolism being leveraged for pathogen-specific mechanisms. However, early studies show that primary metabolic pathways, although shared amongst all organisms, contain intricacies specific to Pseudomonas species that have potential for antibiotic exploitation. Here we lay out some of this work in the hopes that it inspires researchers to continue developing a knowledge base for future antibiotic discovery to build upon and include a case study of a Pseudomonas primary metabolic pathway that has been targeted by small molecules in a species-specific manner.

Global survey of cell death mechanisms reveals metabolic regulation of ferroptosis.

Apoptosis is one type of programmed cell death. Increasingly, non-apoptotic cell death is recognized as being genetically controlled, or 'regulated'. However, the full extent and diversity of alternative cell death mechanisms remain uncharted. Here we surveyed the landscape of pharmacologically accessible cell death mechanisms. In an examination of 56 caspase-independent lethal compounds, modulatory profiling showed that 10 compounds induced three different types of regulated non-apoptotic cell death. Optimization of one of those ten resulted in the discovery of FIN56, a specific inducer of ferroptosis. Ferroptosis has been found to occur when the lipid-repair enzyme GPX4 is inhibited. FIN56 promoted degradation of GPX4. FIN56 also bound to and activated squalene synthase, an enzyme involved in isoprenoid biosynthesis, independent of GPX4 degradation. These discoveries show that dysregulation of lipid metabolism is associated with ferroptosis. This systematic approach is a means to discover and characterize novel cell death phenotypes.

Small molecule-induced oxidation of protein disulfide isomerase is neuroprotective.

Protein disulfide isomerase (PDI) is a chaperone protein in the endoplasmic reticulum that is up-regulated in mouse models of, and brains of patients with, neurodegenerative diseases involving protein misfolding. PDI's role in these diseases, however, is not fully understood. Here, we report the discovery of a reversible, neuroprotective lead optimized compound (LOC)14, that acts as a modulator of PDI. LOC14 was identified using a high-throughput screen of ∼10,000 lead-optimized compounds for potent rescue of viability of PC12 cells expressing mutant huntingtin protein, followed by an evaluation of compounds on PDI reductase activity in an in vitro screen. Isothermal titration calorimetry and fluorescence experiments revealed that binding to PDI was reversible with a Kd of 62 nM, suggesting LOC14 to be the most potent PDI inhibitor reported to date. Using 2D heteronuclear single quantum correlation NMR experiments, we were able to map the binding site of LOC14 as being adjacent to the active site and to observe that binding of LOC14 forces PDI to adopt an oxidized conformation. Furthermore, we found that LOC14-induced oxidation of PDI has a neuroprotective effect not only in cell culture, but also in corticostriatal brain slice cultures. LOC14 exhibited high stability in mouse liver microsomes and blood plasma, low intrinsic microsome clearance, and low plasma-protein binding. These results suggest that LOC14 is a promising lead compound to evaluate the potential therapeutic effects of modulating PDI in animal models of disease.

Passage number is a major contributor to genomic structural variations in mouse iPSCs.

Emergence of genomic instability is a practical issue in preparing neural stem cells (NSCs) and induced pluripotent stem cells (iPSCs). However, it is still not fully understood what the origins and mechanisms for formation are for the genomic alternations observed. Here, we studied the extent of genomic variation on the scale of individual cells originating from the same animal. We used mouse NSCs grown from embryonic cells and iPSCs generated from embryonic brain cells, B cells or fibroblasts, and performed comparative analysis with cultures of fibroblasts from the same mouse. In the first passage of these cell lines, aneuploidies were only observed for chromosomes 6, 11, 12, 19, and Y, which is overall at a rate lower than previously reported; de novo copy number variations (CNVs) were observed in 4.3% of neural iPSCs, 29% of B cell iPSCs, 10% of fibroblast iPSCs, and 1.3% of neurospheres. In contrast, propagation of these first passage cells to a later passage induced additional aneuploidies and CNVs. Breakpoint sequencing analysis suggested that the majority of the detected CNVs arose by replicative mechanisms. Interestingly, we detected identical de novo CNVs in different single cell colonies that appeared to have arisen independently from each other, which suggests a novel CNV formation mechanism in these cells. Our findings provide insights into mechanisms of CNV formation during reprogramming and suggest that replicative mechanisms for CNV formation accompany mitotic divisions.

Linking cytoplasmic dynein and transport of Rab8 vesicles to the midbody during cytokinesis by the doublecortin domain-containing 5 protein.

Completion of mitosis requires microtubule-dependent transport of membranes to the midbody. Here, we identified a role in cytokinesis for doublecortin domain-containing protein 5 (DCDC5), a member of the doublecortin protein superfamily. DCDC5 is a microtubule-associated protein expressed in both specific and dynamic fashions during mitosis. We show that DCDC5 interacts with cytoplasmic dynein and Rab8 (also known as Ras-related protein Rab-8A), as well as with the Rab8 nucleotide exchange factor Rabin8 (also known as Rab-3A-interacting protein). Following DCDC5 knockdown, the durations of the metaphase to anaphase transition and cytokinesis, and the proportion of multinucleated cells increases, whereas cell viability decreases. Furthermore, knockdown of DCDC5 or addition of a dynein inhibitor impairs the entry of Golgi-complex-derived Rab8-positive vesicles to the midbody. These findings suggest that DCDC5 plays an important role in mediating dynein-dependent transport of Rab8-positive vesicles and in coordinating late cytokinesis.

Inhibitors of protein disulfide isomerase suppress apoptosis induced by misfolded proteins.

A hallmark of many neurodegenerative diseases is accumulation of misfolded proteins within neurons, leading to cellular dysfunction and cell death. Although several mechanisms have been proposed to link protein misfolding to cellular toxicity, the connection remains enigmatic. Here, we report a cell death pathway involving protein disulfide isomerase (PDI), a protein chaperone that catalyzes isomerization, reduction and oxidation of disulfides. Through a small molecule screening approach, we discovered five structurally distinct compounds that prevent apoptosis induced by mutant huntingtin protein. Using modified Huisgen cycloaddition chemistry, we then identified PDI as the molecular target of these small molecules. Expression of polyglutamine-expanded huntingtin exon 1 in PC12 cells caused PDI to accumulate at mitochondrial-associated ER membranes and trigger apoptotic cell death via mitochondrial outer-membrane permeabilization. Inhibiting PDI in rat brain cells suppressed the toxicity of mutant huntingtin exon 1 and Aß peptides processed from the amyloid precursor protein. This pro-apoptotic function of PDI represents a new mechanism linking protein misfolding and apoptotic cell death.

Pyochelin Biosynthetic Metabolites Bind Iron and Promote Growth in Pseudomonads Demonstrating Siderophore-like Activity.

Pseudomonads employ several strategies to sequester iron vital for their survival including the use of siderophores such as pyoverdine and pyochelin. Similar in structure but significantly less studied are pyochelin biosynthetic byproducts, dihydroaeruginoic acid, aeruginoic acid, aeruginaldehyde (IQS), and aeruginol, along with two other structurally related molecules, aerugine and pyonitrins A-D, which have all been isolated from numerous Pseudomonad extracts. Because of the analogous substructure of these compounds to pyochelin, we hypothesized that they may play a role in iron homeostasis or have a biological effect on other bacterial species. Herein, we discuss the physiochemical evaluation of these molecules and disclose, for the first time, their ability to bind iron and promote growth in Pseudomonads.

An Efficient Synthesis of 3-Alkylpyridine Alkaloids Enables Their Biological Evaluation.

3-Alkylpyridine alkaloids (3-APAs) isolated from the arctic sponge Haliclona viscosa are a promising group of bioactive marine alkaloids. However, due to limited bioavailability, investigations of their bioactivity have been hampered. Additionally, synthesis of a common intermediate requires the use of protecting groups and harsh conditions. In this work, we developed a simple and concise two-step route to nine different natural and synthetic haliclocyclins. These compounds displayed modest antibiotic activity against several Gram-positive bacterial strains.

Area-level HIV risk and socioeconomic factors associated with willingness to use PrEP among Black people in the U.S. South.

PURPOSE: In the United States (U.S.), southern states have the highest HIV incidence. Uptake of pre-exposure prophylaxis (PrEP) has been slow among Black people, particularly in the South. We know little about how area-level HIV risk influences one's willingness to use PrEP. METHODS: 169 Black participants across 142 ZIP codes in the South completed the 2016 National Survey on HIV in the Black Community. We performed log-binomial regression to estimate the prevalence risk associated with residing in the upper 25th percentile of increases in new HIV diagnosis (2014-2015) within ZIP code and an individual's willingness to use PrEP, adjusting for individual and area-level covariates. RESULTS: Participants were 68% female, mean age of 36 years, and 24% willing to use PrEP. Among the ZIP codes, 23% were within Atlanta, GA. The median increase in new HIV diagnoses was 25 per 100,000 population from 2014 to 2015 (IQR, 14-49). Participants living in ZIP codes within the upper 25th (compared-to-lower 75th) percentile of new HIV diagnoses were more willing to use PrEP (adjusted prevalence ratio (aPR) = 2.02, 95% CI = 1.06-3.86, P = .03). Area-level socioeconomic factors attenuated that association (aPR = 1.63, 95% CI = 0.78-3.39, P = .19). CONCLUSIONS: Area-level factors may influence PrEP uptake among Black people in the South.

Target-Based Design of Promysalin Analogues Identifies a New Putative Binding Cleft in Succinate Dehydrogenase.

Promysalin is a small-molecule natural product that specifically inhibits growth of the Gram-negative pathogen Pseudomonas aeruginosa (PA). This activity holds promise in the treatment of multidrug resistant infections found in immunocompromised patients with chronic illnesses, such as cystic fibrosis. In 2015, our lab completed the first total synthesis; subsequent analogue design and SAR investigation enabled identification of succinate dehydrogenase (Sdh) as the biological target in PA. Herein, we report the target-guided design of new promysalin analogues with varying alkyl chains, one of which is on par with our most potent analogue to date. Computational docking revealed that some analogues have a different orientation in the Sdh binding pocket, placing the terminal carbon proximal to a tryptophan residue. This inspired the design of an extended side chain analogue bearing a terminal phenyl moiety, providing a basis for the design of future analogues.

Opioid overdose deaths and potentially inappropriate opioid prescribing practices (PIP): A spatial epidemiological study.

INTRODUCTION: Opioid overdose deaths quintupled in Massachusetts between 2000 and 2016. Potentially inappropriate opioid prescribing practices (PIP) are associated with increases in overdoses. The purpose of this study was to conduct spatial epidemiological analyses of novel comprehensively linked data to identify overdose and PIP hotspots. METHODS: Sixteen administrative datasets, including prescription monitoring, medical claims, vital statistics, and medical examiner data, covering >98% of Massachusetts residents between 2011-2015, were linked in 2017 to better investigate the opioid epidemic. PIP was defined by six measures: ≥100 morphine milligram equivalents (MMEs), co-prescription of benzodiazepines and opioids, cash purchases of opioid prescriptions, opioid prescriptions without a recorded pain diagnosis, and opioid prescriptions through multiple prescribers or pharmacies. Using spatial autocorrelation and cluster analyses, overdose and PIP hotspots were identified among 538 ZIP codes. RESULTS: More than half of the adult population (n = 3,143,817, ages 18 and older) were prescribed opioids. Nearly all ZIP codes showed increasing rates of overdose over time. Overdose clusters were identified in Worcester, Northampton, Lee/Tyringham, Wareham/Bourne, Lynn, and Revere/Chelsea (Getis-Ord Gi*; p < 0.05). Large PIP clusters for ≥100 MMEs and prescription without pain diagnosis were identified in Western Massachusetts; and smaller clusters for multiple prescribers in Nantucket, Berkshire, and Hampden Counties (p < 0.05). Co-prescriptions and cash payment clusters were localized and nearly identical (p < 0.05). Overlap in PIP and overdose clusters was identified in Cape Cod and Berkshire County. However, we also found contradictory patterns in overdose and PIP hotspots. CONCLUSIONS: Overdose and PIP hotspots were identified, as well as regions where the two overlapped, and where they diverged. Results indicate that PIP clustering alone does not explain overdose clustering patterns. Our findings can inform public health policy decisions at the local level, which include a focus on PIP and misuse of heroin and fentanyl that aim to curb opioid overdoses.