Immune molecule may drive excessive drinking in alcohol use disorder

Good news, but progess on this subject is slow!

"The drugs that keep rheumatoid arthritis in check may one day help people stop drinking. A new ... study shows that an anti-inflammatory molecule, already approved by the U.S. Food and Drug Administration to treat autoimmune diseases, reduces excessive alcohol consumption in alcohol-dependent female mice. ..."

From the abstract:

"Alcohol use disorder (AUD) is one of the most prevalent mental health disorders worldwide yet effective therapeutics remain limited.

Mounting evidence indicates that dysregulated immune signaling in the brain plays a role in AUD pathophysiology. Activation of pro-inflammatory pathways like the interleukin-6 (IL-6) pathway represents a potential point of convergence between synaptic dysfunction and motivational changes in AUD that remain undiscovered.

Thus, using a translational neuroscience approach and well-established model of chronic alcohol intake, we investigated the cell-type specific role of IL-6 signaling in the central amygdala, a critical region in the development and maintenance of alcohol dependence.

We demonstrate that chronic alcohol exposure recruits IL-6-related pathways in humans and rodents via astrocytic, neuronal, and microglial mechanisms, and that IL-6 inhibits central amygdala GABAergic transmission.

Notably, systemic administration of an IL-6 receptor antibody decreased alcohol drinking in alcohol-dependent female mice.

Collectively, our findings support IL-6 inhibition as a novel-neuroimmune-targeted therapeutic strategy to reduce excessive drinking in the context of AUD."

Immune molecule may drive excessive drinking in alcohol use disorder | Scripps Research "Scripps Research scientists showed that blocking an immune molecule tied to inflammation reduced alcohol consumption in mice."

Translational evidence for increased central amygdala IL-6 activity in alcohol dependence (open access)

Fig 1 IL-6 signaling pathway and overall experimental timeline.

A new vaccine that teaches the immune system to rapidly neutralize fentanyl and new emerging synthetic fentanyl analogs

Good news!

"... Now, scientists at Scripps Research have shown the feasibility of a completely different approach to combating fentanyl deaths: a vaccine that teaches the immune system to rapidly neutralize the drug before it reaches the brain in the first place. The research ... suggests that their vaccine candidate could work against not only fentanyl itself, but most fentanyl-related “designer drugs”—altered versions of fentanyl made to boost its effects or evade detection. ...

When the team tested the resulting antibodies against different fentanyl designer drugs, the vaccine showed exactly the kind of pan specificity they had been looking for. The antibodies bound tightly to fentanyl and other dangerous variants—including carfentanil, China White, acetylfentanyl and furanylfentanyl. Yet they ignored clinically used opioids like morphine, oxycodone, remifentanil and alfentanil. 

More importantly, when vaccinated mice were given fentanyl doses that would normally cause severe respiratory depression, the animals’ breathing remained nearly normal. Measurements of fentanyl concentration in the brain showed that the vaccine had reduced levels there by roughly 70% compared to mice that didn’t receive the vaccine. ..."

From the abstract:

"Synthetic opioids pose a chemically evolvable threat, in which extreme potency and rapid diversification allow fentanyl analogues to outpace structure-specific countermeasures. Immune strategies largely responded by copying the parent chemotype, implicitly treating small-molecule recognition as scaffold-dependent. Here, we examined an alternative hypothesis: adaptive immunity can recover fentanyl-class identity from transferable spatial and physicochemical information. Replacing the canonical piperidine of fentanyl with a 2-azaspiro[3.3]heptane, we created a chemically orthogonal immunogen with a radically altered three-dimensional arrangement.

Despite this, vaccination elicited high-titer cross-reactive antibodies, broad fentanyl-analogue binding, and protection matching a fentanyl-derived benchmark. Fentanyl antinociception shifted into the ∼1.1–2.1 mg kg–1 range, preserved ventilation during respiratory challenge, and reduced brain fentanyl from 61.9 ± 10.0 to 17.2 ± 0.7 nM.

These results reveal programmable antibody recognition, demonstrating that molecular class identity arises not from direct structural mimicry but through higher-order spatial and physicochemical relationships."

A fentanyl countermeasure that adapts to combat future black-market drugs | Scripps Research "Scripps Research scientists developed a vaccine that teaches the immune system to rapidly neutralize fentanyl and new emerging synthetic fentanyl analogs."

Redefining Drug Immune Recognition: A Radically Reconfigured Molecular Architecture Enables Broad Fentanyl-Class Protection (no public access)

Graphical abstract (?)

Fentanyl (yellow structure) and the antibody's binding pocket (green structure)—showing how the antibody recognizes the overall shape of the new molecule, rather than one particular scaffold.

Scientists build an “evolution engine” to rapidly reprogram proteins

Good news! Are we on the cusp of outdoing evolution? You bet!

"... The system, named T7-ORACLE ... represents a breakthrough in how researchers can engineer therapeutic proteins for cancer, neurodegeneration and essentially any other disease area.

“This is like giving evolution a fast-forward button,”  ... “You can now evolve proteins continuously and precisely inside cells without damaging the cell’s genome or requiring labor-intensive steps.” ..."

From the editor's summary and abstract:

"Editor’s summary

Continuous evolution of proteins in the lab is often slow because normal mutation rates in bacteria are very low. Diercks et al. investigated whether a highly mutagenic DNA replication system could speed up evolution in Escherichia coli without harming the host genome. They engineered an orthogonal T7 replisome that replicates only target plasmids at mutation rates 100,000 times higher than normal while leaving the rest of the genome unchanged. Using this system, the authors rapidly evolved TEM-1 β-lactamase to gain much stronger resistance to several antibiotics in under a week. This approach could greatly accelerate protein engineering and antibiotic resistance studies. ...

Abstract

Systems that perform continuous hypermutation of designated genes without compromising the integrity of the host genome can substantially accelerate the evolution of new or enhanced protein functions.

We describe an orthogonal DNA replication system in Escherichia coli based on the controlled expression of the replisome of bacteriophage T7 (T7-ORACLE).

The system replicates circular plasmids that enable high transformation efficiencies and seamless integration into standard molecular biology workflows. Engineering of T7 DNA polymerase yielded variant proteins with mutation rates of 1.7 × 10−5 substitutions per base in vivo—100,000-fold above the genomic mutation rate. We demonstrated continuous evolution using the T7 replisome by expanding the substrate scope of TEM-1 β-lactamase and increasing activity 5000-fold against clinically relevant monobactam and cephalosporin antibiotics in less than 1 week."

Scientists build an “evolution engine” to rapidly reprogram proteins | Scripps Research "A new platform developed at Scripps Research enables fast, scalable protein evolution—opening the door to new therapies and diagnostics, and to predicting resistance mutations across many disease areas."

An orthogonal T7 replisome for continuous hypermutation and accelerated evolution in E. coli (no public access)

An Orthogonal T7 Replisome for Continuous Hypermutation and Accelerated Evolution in E. coli (preprint, open access)

Fig. 1 Establishing an orthogonal replication system in E. coli based on the bacteriophage T7 replisome.

Enzyme engineering opens door to novel therapies for Parkinson’s, cancers and other hard-to-target protein diseases

Good news! This could become a powerful new treatment option! This seems to be very promising.

"Now, a new study ... demonstrates a proof of concept for a new strategy: engineering proteases—enzymes that cut proteins at specific sites—to selectively degrade these elusive targets with high precision in the proteome of human cells. ...

the study shows how to reprogram a protease from botulinum toxin to target α-Synuclein—a protein with unstructured regions used here as a model. The study marks one proof point in a broader approach that could be applied to a wide range of targets across the proteome. 

“This work highlights how we can use the power of laboratory evolution to engineer proteases that offer a new way to treat diseases caused by hard-to-target proteins,” ...

To reprogram this precision for α-Synuclein, the research team modified the enzyme using directed evolution, a laboratory process that involves introducing mutations and selecting variants with improved function over multiple cycles.

The result: Protease 5. The challenge, however, wasn’t just reprogramming the protease to target α-Synuclein—it was ensuring that it attacked only α-Synuclein and nothing else. Past attempts to evolve proteases for therapeutic use have resulted in enzymes that targeted too broad a range of proteins, cleaving multiple unintended molecules and causing toxicity in cells.

“α-Synuclein is an incredibly hard protein to target because it doesn’t have a stable structure,”  ...

Although α-Synuclein plays a central role in Parkinson’s disease and related disorders, it was used in this study as a model protein representing a broader class known as intrinsically disordered proteins (IDPs)—proteins that lack a defined shape and are notoriously difficult to target with drugs. This instability makes such illnesses challenging to treat because traditional therapies typically work by attaching to stable pockets on proteins, like a key fitting inside a lock. However, α-Synuclein has no such binding site, leaving few viable treatment options. “That’s where proteases come in,” ... “Instead of needing a specific binding site, they can be engineered to recognize and cut α-Synuclein directly, preventing it from dangerously accumulating in the brain.” 

Using directed evolution, the team stepwise modified the botulinum protease, selecting variants that showed increasing preference for α-Synuclein. “Directed evolution works like selective breeding—just as farmers breed plants for better crops, scientists guide proteins through many small changes, choosing the best version at each step,” ... “Each round of modifications made the enzyme more specialized,” ... “until it could selectively degrade α-Synuclein while leaving other proteins untouched.”

When tested in human cells, Protease 5 nearly eliminated all α-Synuclein proteins, suggesting it could help prevent the harmful buildup seen in Parkinson’s disease. And because the enzyme was designed to precisely target α-Synuclein, it didn’t cause toxicity or disrupt essential cellular functions.  ..."

From the significance and abstract:

"Significance

The ability to evolve proteases that selectively cleave a desired protein in vivo could provide access to useful therapeutic agents.

This would be especially powerful when targeting intrinsically disordered proteins (IDPs), a hard-to-drug class of proteins involved in many human diseases including cancer and neurodegenerative diseases.

Here, we demonstrate the stepwise evolution of clinically used botulinum protease to proteolyze the IDP α-Synuclein which forms plaques in the brains of patients suffering from Parkinson’s disease.

Abstract

There is considerable interest in the targeted degradation of proteins implicated in human disease.

The use of sequence-specific proteases for this purpose is severely limited by the difficulty in engineering the numerous enzyme–substrate interactions required to yield highly selective proteases while maintaining catalytic activity.

Herein, we report a strategy to evolve a protease for the programmed degradation of α-Synuclein, a presynaptic protein closely linked to Parkinson’s disease. Our structure-guided evolution campaign uses the protease from botulinum neurotoxin and showcases the stepwise change of specificity from its native substrate SNAP25 to the selective degradation of α-Synuclein.

The protease’s selectivity is further demonstrated in human cells where near complete degradation of overexpressed human α-Synuclein is observed with no significant effects on cell proliferation. This stepwise strategy may serve as a general approach to evolve highly selective proteases targeting dysregulated proteins."

Enzyme engineering opens door to novel therapies for Parkinson’s, cancers and other hard-to-target protein diseases | Scripps Research "Researchers reprogrammed a botulinum toxin protease to selectively break down disease-causing proteins in human cells, providing proof of concept for developing new therapies for a wide range of illnesses."

Revolutionary Enzyme Engineering Paves the Way for Innovative Treatments in Parkinson’s Disease, Cancer, and Challenging Protein Disorders

Targeted degradation of α-Synuclein using an evolved botulinum toxin protease (no public access)

It takes two to tango: What a protein’s “dance” reveals about human health

Very recommendable!

Excerpt: "“I eat and breathe proteins,” she jokes."

"... we developed an algorithm to predict a protein’s different conformations. We have shown over and over that these conformational substates are essential for biological function. That means that learning how proteins “dance” is key to understanding the difference between health and disease. ...

why certain protein language models work. The models we investigated are fed a single protein sequence and then predict what the corresponding 3-D structure looks like. Yet, how they arrive at these conclusions was a “black box” of sorts.

In this paper, we were determined to figure out how these models learn and predict, if we are to use them reliably as a field.  ... The third one—which turned out to be true—is that it learned to find paired interacting protein fragments, including whole segments.  

Big picture, we shed light into the question of how these protein language models learn. On the more technical side, we determined how long the protein segments must be for the model to identify the correct 3-D structure. Machine learning language models, including the Nobel Prize-winning AlphaFold, are so hot right now because solving protein structures with a single sequence has been a monumental breakthrough. ...

Protein language models like AlphaFold are limited because they only come up with one structure. The “signal” for the other protein structure—the one it “dances” between—gets diluted. ...

using the protein KaiB as a benchmark. KaiB is essential for regulating circadian rhythm in certain bacteria ... KaiB only has two protein conformations, and if you put it in a test tube with its partner KaiC, they create a 24-hour oscillation—the underlying mechanism we revealed in another Nature paper in early 2023. In this Nature paper, however, we had only predicted KaiB’s two end states—not the actual dynamics, or pathway, of how it went from one conformation to the other. 

In our new PNAS study, we looked at exactly how KaiB “travels over the mountain,” so to speak. In other words, how it climbs over the free energy landscape. ...

First of all, we figured out that KaiB’s conversion to its alternate state takes hours. ... The speed of any protein conformational transition is tuned to the biological function needed. The KaiB protein controls the organism’s 24-hour clock, meaning it needs to move super, super slow. In our paper, we saw what evolution had to do to slow this process down.

We studied these changes using nuclear magnetic resonance (NMR)—an amazing method where you can measure protein dynamics in solution at atomic resolution—and we found that KaiB’s conversion takes three hours to be completed. And then we determined the atomistic pathway, which was very complicated. At the high level, we figured out how evolution tunes protein kinetics to align with its overall function. ..."

From the significance and abstract:

"Significance

Protein language models (pLMs) have exhibited remarkable capabilities in protein structure prediction and design. However, the extent to which they comprehend the intrinsic biophysics of protein structures remains uncertain. We present a suite of analyses that dissect how the flagship pLM ESM-2 predicts structure. Motivated by a consistent error of protein isoforms predicted as structured fragments, we developed a completely unsupervised method to uniformly evaluate any pLM, allowing us to compare coevolutionary statistics to linear models. We further identified that ESM-2 does not require full context for predicting interresidue contacts. Our study highlights the current limitations of pLMs and contributes to a deeper understanding of their underlying mechanisms, paving the way for more reliable protein structure predictions.

Abstract

Protein language models (pLMs) have emerged as potent tools for predicting and designing protein structure and function, and the degree to which these models fundamentally understand the inherent biophysics of protein structure stands as an open question. Motivated by a finding that pLM-based structure predictors erroneously predict nonphysical structures for protein isoforms, we investigated the nature of sequence context needed for contact predictions in the pLM Evolutionary Scale Modeling (ESM-2). We demonstrate by use of a “categorical Jacobian” calculation that ESM-2 stores statistics of coevolving residues, analogously to simpler modeling approaches like Markov Random Fields and Multivariate Gaussian models. We further investigated how ESM-2 “stores” information needed to predict contacts by comparing sequence masking strategies, and found that providing local windows of sequence information allowed ESM-2 to best recover predicted contacts. This suggests that pLMs predict contacts by storing motifs of pairwise contacts. Our investigation highlights the limitations of current pLMs and underscores the importance of understanding the underlying mechanisms of these models."

It takes two to tango: What a protein’s “dance” reveals about human health - Scripps Research Magazine

Protein language models learn evolutionary statistics of interacting sequence motifs (open access)

A graphic depicting how KaiB converts to its alternate states and “climbs” over the free energy landscape.

Fig. 1 Three hypotheses of how language models predict protein structures.

Fig. 2 Deep learning structure-based methods predict isoforms as fragments of full-length structures with exposed aggregation-prone residues. 

Newly discovered node in the brain could help scientists understand dysfunctional social behavior

Recommendable! Our brain is still terra incognita!

"... A group of scientists discovered a node in the brains of male mice that modulates the sounds they make in social situations. This discovery, published in Nature, could help identify similar locations in the human brain, and potentially lead to a better understanding of social disorders such as autism or depression. ... Most research on noise production in the brain has focused on language development ... But the sounds that even an infant can make—a giggle, a cry, a scream—don’t have to be learned and are just as vital for communication. Identifying how the brain decides on these responses is the first step to understanding where things can go wrong in social behavioral disorders such as autism and depression. ..."

"... Here we identify mouse neurons from the lateral preoptic area (LPOA) that express oestrogen receptor 1 (LPOAESR1 neurons) and, when activated, elicit the complete repertoire of [innate courtship ultrasonic vocalizations USV] syllables emitted during natural courtship. ..."

Newly discovered node in the brain could help scientists understand dysfunctional social behavior | Scripps Research The discovery could lead to a better understanding of, and more targeted treatments for, social disorders such as depression and autism.

Here is the link to the underlying research paper:

Flexible scaling and persistence of social vocal communication (no public access)

Discovery points to possible new treatment strategy for Parkinson’s disease and Lewy body dementia

Good news!

"... The researchers also found, for the first time, that an experimental drug called NitroSynapsin can prevent this harmful effect by blocking excessive activity of the neuronal glutamate receptors, while leaving normal synaptic activity essentially unchanged. NitroSynapsin is meant to be an improved version of the drug memantine (marketed as Namenda®), which Lipton previously developed and patented for neurodegenerative disorders and is currently FDA-approved for Alzheimer’s disease. ..."

"... Loss of synaptic function and ensuing neuronal loss are associated with disease progression in Parkinson's disease (PD), Lewy body dementia (LBD), and other neurodegenerative diseases. However, the mechanism of synaptic damage remains incompletely understood. α-Synuclein (αSyn) misfolds in PD/LBD, forming Lewy bodies and contributing to disease pathogenesis. Here, we found that misfolded/oligomeric αSyn releases excessive astrocytic glutamate, in turn activating neuronal extrasynaptic NMDA receptors (eNMDARs), thereby contributing to synaptic damage. Additionally, αSyn oligomers directly activate eNMDARs, further contributing to damage. ..."

Discovery points to possible new treatment strategy for Parkinson’s disease and Lewy body dementia | Scripps Research Scientists find evidence that clusters of proteins associated with Parkinson’s and other diseases can induce a toxic process involving glutamate, a neurotransmitter.

Here is the link to the underlying research paper:

α-Synuclein Oligomers Induce Glutamate Release from Astrocytes and Excessive Extrasynaptic NMDAR Activity in Neurons, Thus Contributing to Synapse Loss

A new clue to the cause of ALS and frontotemporal dementia

Good news! Hopefully, a breakthrough!

"... reactive nitrogen molecules in the human brain. These reactive molecules, which naturally increase in the brain with aging, can set off a damaging process in which an important protein, known as TDP-43, clumps together and loses its function in affected brain cells. ..."

"... in the absence of mutation (i.e., in the vast majority of “sporadic” cases), mechanisms for protein misfolding/aggregation remain largely unknown. Here, we show environmentally induced nitrosative stress triggers protein aggregation and cell-to-cell spread. In patient brains with amyotrophic lateral sclerosis (ALS)/frontotemporal dementia (FTD), aggregation of the RNA-binding protein TDP-43 constitutes a major component of aberrant cytoplasmic inclusions. We identify a pathological signaling cascade whereby reactive nitrogen species cause S-nitrosylation of TDP-43 (forming SNO-TDP-43) to facilitate disulfide linkage and consequent TDP-43 aggregation. Similar pathological SNO-TDP-43 levels occur in postmortem human FTD/ALS brains and in cell-based models, including human-induced pluripotent stem cell (hiPSC)-derived neurons. ..."

A new clue to the cause of ALS and frontotemporal dementia | Scripps Research Scientists find evidence that reactive nitrogen molecules, abundant in old age, can trigger the disease process for two highly fatal conditions.

Here is the link to the underlying research paper:

S-nitrosylated TDP-43 triggers aggregation, cell-to-cell spread, and neurotoxicity in hiPSCs and in vivo models of ALS/FTD

Super-potent human antibodies protect against COVID-19 in animal tests

Great news! This is the beginning of the end of the scourge of microbes causing diseases! Human ingenuity needs to defeat pathogenic viruses and bacteria once and for all!!!

Super-potent human antibodies protect against COVID-19 in animal tests | Scripps Research Scientists isolate powerful coronavirus-neutralizing antibodies from COVID-19 patients and successfully test in animals, all in less than seven weeks.

Huntington’s disease progression involves DNA damage sensor

Good news! We may be getting closer to a cure!



"A new study ... provides new insights into the molecular events that lead to the progressive destruction of brain cells in Huntington’s. The research reveals a central role for a damage-sensing enzyme called cGAS that seems to ignite a cascade of inflammation and excessive cellular housekeeping, a process called autophagy. Their study, a ... raises the possibility that reducing cGAS activity in the brain may be a treatment strategy worth testing in further studies ..."



Huntington’s disease progression involves DNA damage sensor | Scripps Research Abnormal cellular housekeeping and inflammation point to potential target for treating fatal neurodegenerative disorder.

Scripps Research Institute Enters Presidential Election Campaign Exploiting Racism

Another leftist academic moron has come out with propaganda and demagoguery regarding race in America. Apparently, we are in a presidential election year. Stoking race tensions has now become part of it!



This time it is James Williamson, PhD, Executive Vice President, Research and Academic Affairs, Scripps Research, La Jolla, California



"Black Lives Matter." All lives matter you ignorant fool!



"We understand that Black members of our community are hurting, and please know that we see you, we care about you, and we are here for you. We see the momentum of support for the Black community swelling, and we will be a part of that. We insist that we use this time of crisis as a catalyst for change."

This is so pathetic, it is beyond words!





email : Webview : Scientists in solidarity

Clues to COVID-19 coronavirus’s vulnerability emerge from an antibody against SARS | Scripps Research

Good news!

"An antibody recovered from a survivor of the SARS epidemic in the early 2000s has revealed a potential vulnerability of the new coronavirus at the root of COVID-19 ... The structural mapping revealed a nearly identical site on both coronaviruses to which the antibody [anti-SARS-CoV antibody called CR3022] binds, suggesting a functionally important and vulnerable site for this family of coronaviruses. ... That high degree of similarity implies that the site has an important function that would be lost if it mutated significantly. Yet, the site’s function remains mysterious. ... The Wilson lab is known for its pioneering structural studies of antibodies bound to viruses including HIV and influenza. These studies have been used to inform designs of vaccines and antibody drugs, as well as other therapeutics. ... "
Clues to COVID-19 coronavirus’s vulnerability emerge from an antibody against SARS | Scripps Research

All shook up: Researchers mix RNA and DNA to study how life’s process began billions of years ago

Recommendable! Mixture of RNA and DNA versus RNA World hypothesis!

This goes way beyond the famous primordial soup experiment (aka as Miller-Urey experiment) of the 1950s.

"“That's not the case, because RNA World relies on RNA replicating itself, which is very difficult."
Part of the challenge is that RNA molecules form stable structures called duplexes. These structures have what’s known as a strong binding affinity. This means the RNA molecules have difficulty separating from each other and acting as templates for replicating further in the absence of enzymes. 
... now has experimental evidence to demonstrate that life’s process on Earth could have actually started with molecules that looked like a mixture of RNA and DNA. ... report that these mixed molecules form unstable duplexes and have lesser affinity for themselves. Surprisingly, these “chimeras” have stronger affinity for RNA and DNA, which allows them to act as templates for making RNA or DNA."

All shook up: Researchers mix RNA and DNA to study how life’s process began billions of years ago | Scripps Research

New screening method identifies potential anticancer compounds that reawaken T cells

Cancer is history!

"Cancerous tumors often thrive because they render T cells dysfunctional or “exhausted.” The new method uncovers medicinal compounds that can restore the function of these T cells, making cancers vulnerable to them again. ... The scientists demonstrated the potential utility of the approach by using it to rapidly screen a collection of more than 12,000 drug compounds—uncovering 19 that can reawaken exhausted T cells. ... but also to quickly analyze these T cells to determine how these compounds work on them ... A unique variant of LCMV [lymphocytic choriomeningitis virus] known as “clone 13” establishes a persistent infection by exhausting the virus-specific T cells that are required to clear the infection. It does this by boosting signals through T-cell receptors such as PD-1 and IL-10. The discovery that LCMV clone 13 can survive by switching off anti-LCMV T cells was quickly followed by the recognition that cancers often persist using the same trick."

New screening method identifies potential anticancer compounds that reawaken T cells | Scripps Research The technique may be useful in developing new combination-immunotherapy regimens against cancers and persistent infections.