science

Protease enzymes have a long, well-documented history that runs in parallel with the rise of modern biochemistry. The story begins in the 19th century with simple physiological observations about digestion and blood clotting and then accelerates in the 20th century as chemists and crystallographers proved that enzymes are real, isolable proteins and later worked out how proteases work at atomic detail.

The first protease to be recognized was pepsin, identified in 1836 by the German physiologist Theodor Schwann. Schwann observed that an acidic substance in gastric juice could dissolve proteinaceous food and he gave it the name “pepsin” (from the Greek for digestion), marking the first time a specific substance was associated with a chemical process of the body rather than with a living tissue as a whole. (Encyclopedia Britannica) Around the same period investigators were also noting that blood could be converted into a fibrous clot by an “enzymatic” action; Alexander Schmidt proposed in 1872 that an enzyme (which he called thrombin) converted fibrinogen to fibrin, an insight that set the stage for later work on the coagulation cascade. (MDPI)

The mid- to late-1800s saw further identification of digestive proteases. In 1876 the German physiologist Wilhelm Kühne isolated and named trypsin from pancreatic juice and helped popularize the term “enzyme” for these non-cellular ferments. Kühne’s work established that different organs produced distinct proteolytic activities with different chemical properties. (PMC)

Although pepsin, trypsin and related proteolytic activities were known for decades, a fundamental conceptual leap occurred in the early 20th century when enzymologists began to purify enzymes and to ask what enzymes actually were made of. James B. Sumner’s crystallization of urease in 1926 demonstrated that an enzyme could be obtained in crystalline form and behave like a pure chemical substance; Sumner concluded that enzymes were proteins, a result that was later reinforced when John H. Northrop crystallized pepsin, trypsin and chymotrypsin around 1929–1930. For this body of work Sumner, Northrop and Wendell Stanley were awarded the Nobel Prize in Chemistry in 1946. Those achievements moved enzymes — and proteases in particular — from physiological curiosities to definable molecular entities that could be studied chemically and structurally. (NobelPrize.org)

With purification and crystallization established, the mid-20th century concentrated on mechanism and structure. The serine proteases (trypsin, chymotrypsin, elastase and relatives) became model systems for enzymology, and in the 1960s crystallographers produced three-dimensional structures of chymotrypsin and related enzymes that revealed the classic “catalytic triad” and the oxyanion hole—key mechanistic features explaining how these proteins accelerate peptide-bond hydrolysis. At the same time, investigators refined systematic ways to describe protease specificity; the influential Schechter–Berger notation (introduced in 1967) standardized how cleavage sites and enzyme subsites are labeled (P1/P1′, S1/S1′ etc.), which greatly helped comparative and mechanistic work. (PubMed)

Parallel threads of discovery broadened the protease story. Researchers characterized different catalytic classes (serine, cysteine, aspartic, and metalloproteases) and cataloged large protease families with distinct evolutionary origins and biological roles. Work on blood coagulation in the first half of the 20th century mapped a cascade of proteolytic activations (many involving zymogens, inactive precursors that are activated by proteolysis), which explained how a single enzymatic trigger can be amplified into clot formation and later regulated by specific inhibitors. (PubMed)

Clinical and genetic findings also shaped protease biology. During the 20th century the discovery of endogenous protease inhibitors and their deficiencies—most notably alpha-1 antitrypsin (AAT) deficiency linked to early-onset emphysema—illustrated how an imbalance between proteases and their inhibitors causes disease and focused attention on protease regulation as medically important. Advances in molecular genetics, protein chemistry and later recombinant methods in the 1970s–1990s expanded both the list of known human proteases and the ability to manipulate them for therapy. (PubMed)

In recent decades protease research has become highly interdisciplinary. Structural biology, high-throughput substrate profiling, and genome sequencing revealed huge protease repertoires across life and clarified roles in immunity, development, cancer, and pathogen biology. Proteases are now both laboratory tools and clinical agents: they serve as diagnostic markers, therapeutic targets (for example in clotting disorders, hepatitis C protease inhibitors, and cancer), and, in some cases, as administered enzymes for replacement therapy or wound debridement. Contemporary reviews and historical retrospectives highlight how an observation about “something in stomach juice” in 1836 grew into a molecular field that underpins major areas of physiology and medicine. (PubMed)

Taken together, the history of proteases illustrates a classic arc in life-science discovery: descriptive physiology gave names and phenomena in the 19th century; purification and proof that enzymes are proteins took place in the early 20th century; structural and mechanistic understanding arrived in the mid-20th century; and molecular, genetic, and therapeutic applications have followed in the late 20th and early 21st centuries.

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The molecules trigger a built-in cellular stress response and show promise as broad-spectrum antivirals against Zika, herpes, RSV, and more.

Researchers at MIT and other institutions have identified compounds that can fight off viral infection by activating a defense pathway inside host cells. These compounds, they believe, could be used as antiviral drugs that work against not just one but any kind of virus.

The researchers identified these compounds, which activate a host cell defense system known as the integrated stress response pathway, in a screen of nearly 400,000 molecules. In tests in human cells, the researchers showed that the compounds help cells fend off infection from RSV, herpes virus, and Zika virus. They also proved effective in combating herpes infection in a mouse model.

The research team now plans to test the compounds against additional viruses, in hopes of developing them for eventual clinical trials.

“We’re very excited about this work, which allows us to harness the stress response of the host cells to arrive at a means to identify and develop broad-spectrum antivirals,” says James Collins, the Termeer Professor of Medical Engineering and Science in MIT’s Institute for Medical Engineering and Science (IMES) and Department of Biological Engineering.

Collins and Maxwell Wilson, an associate professor of molecular biology at the University of California, Santa Barbara and chief scientific officer of Integrated Biosciences, are the senior authors of the new study, which appears in Cell. Felix Wong, a former MIT postdoc and chief executive officer of Integrated Biosciences, is the lead author of the paper. In addition to MIT, UCSB, and Integrated Biosciences, the research team also includes scientists from Illumina Ventures and Princeton University.

Boosting cell defense

In human cells, the integrated stress response pathway is turned on in response to viral infection as well as other types of stress such as starvation. During viral infection, the pathway is triggered by double-stranded RNA, a molecule produced during the replication cycle of viruses. When that RNA is detected, the cell shuts down protein synthesis, which blocks the virus from producing the proteins it needs to replicate.
Compounds that boost this pathway, the researchers believe, could be good candidates for new antiviral drugs that could combat any type of virus.

“Typically, how antivirals are developed is that you develop one antiviral for one specific virus,” Wong says. “In this case, we hypothesized that being able to modulate the host cell stress response might give us a new class of broad-spectrum antivirals — compounds that directly act on the host cells to alter something fundamental about how all viruses replicate.”

To help them identify compounds that would enhance the activity of this pathway during viral infection, the researchers invented a novel optogenetic screen. Optogenetics is a bioengineering technique that allows researchers to insert light-sensitive proteins into the genome of a cell. In this case, the researchers engineered modifications to a protein called PKR, which turns on the stress pathway, so that they could turn it on with light.

Using this technique, the researchers screened a library of nearly 400,000 commercially available and proprietary chemical compounds. Each of these compounds was applied to human cells as the cells were also exposed to blue light, which simulated viral infection by activating PKR.

By measuring the cells’ survival rates, the researchers could determine which compounds boosted activation of the pathway and amplified the cells’ ability to shut down viral reproduction. This screen yielded about 3,500 compounds with potential antiviral activity, which were evaluated further.

“If the pathway were turned on in response to viral infection, what our compounds do is they turn it on full blast,” Wong says. “Even in the presence of a small amount of virus, if the pathway is triggered, then the antiviral response is also maximized.”

Fighting infection

The researchers then selected eight of the most promising compounds and screened them for their ability to kill viruses while avoiding harmful effects in human cells. Based on these tests, the researchers chose three top candidates, which they called IBX-200, IBX-202, and IBX-204.

In cells that were infected with either Zika virus, herpes virus, or RSV, treatment with these compounds significantly reduced the amount of virus in the cells. The researchers then tested one of the compounds, IBX-200, in mice infected with herpes virus, and found that it was able to reduce the viral load and improve symptoms.

Experiments showed that these compounds appear to turn on an enzyme that is involved in detecting stress. This activates the stress response pathway and primes the cells to become more responsive to viral infection. When applied to cells that are not already infected, the compounds have no effect.

The researchers now plan to evaluate their lead candidates against a broader range of viruses. They also aim to identify additional compounds that activate the integrated stress response, as well as other cellular stress pathways with the potential to clear viral or bacterial infections.

The research was funded by the Defense Threat Reduction Agency, the National Science Foundation, the U.S. Army Research Office, and Integrated Biosciences.

(Source : MITNews)

L-glutamine is an amino acid your body normally makes, but during stress, illness, or heavy training your tissues can use more than your body can produce — so it becomes “conditionally essential.” Explaining what it does and why people take it becomes easier if we look at three plain facts: what glutamine is used for inside cells, which tissues rely on it most, and what the clinical evidence actually supports.

Inside cells, glutamine is a versatile fuel and building block. It donates nitrogen for making other amino acids and nucleotides (the building blocks of DNA/RNA), it’s a precursor for glutamate (an important neurotransmitter) and for glutathione (the body’s major antioxidant), and it provides carbon and energy for rapidly dividing or highly active cells. Because of these roles, glutamine is especially important for cells that turn over fast or need extra energy: the cells lining the intestine (enterocytes), many immune cells (like lymphocytes and macrophages), and muscle tissue during recovery.

Those cellular roles help explain the main health benefits suggested by research and clinical use. For the gut, supplemental L-glutamine can support the integrity of the intestinal lining and reduce permeability (sometimes called “leaky gut”) in situations where the gut is stressed — for example after major surgery, during severe infections, or certain inflammatory gut conditions. By helping enterocytes stay healthy and repair themselves, glutamine can reduce symptoms that stem from impaired gut barrier function and has been used to lessen treatment-related gut damage (for instance, some studies report it reduces mucositis from chemotherapy).

For the immune system, glutamine serves as a preferred fuel for many immune cells. During severe illness or injury the body’s glutamine demand rises, and providing extra glutamine can help immune cells function better in some clinical situations, which may improve recovery after trauma or extensive surgery. In sports and exercise settings, the idea is similar: because heavy, prolonged exercise temporarily stresses immune function and muscle tissue, glutamine supplementation is sometimes used to support recovery. The evidence here is mixed — some studies find small benefits for reducing short-term soreness or improving markers of recovery, while many others find little or no performance advantage in healthy athletes.

Muscle and metabolic effects are another angle. Glutamine helps shuttle nitrogen between tissues and can support positive nitrogen balance, which matters for wound healing and rebuilding tissue after catabolic stress. It’s also involved in glucose metabolism under certain conditions, so it can be an energy source when the body is stressed. Clinically, glutamine has been used as part of nutritional regimens for people who are critically ill, recovering from burns, or after major surgery, where it can help reduce complications and support healing — again, with the strongest evidence in specific, high-stress medical settings rather than as a general fitness “booster.”

It’s important to be clear about the limits of the evidence. For healthy people taking glutamine to “boost immunity” or to get large performance gains, the scientific support is weak and inconsistent. The clearest benefits appear in controlled medical contexts: supporting gut integrity and immune function in people who are ill, injured, or undergoing intensive medical treatments. For athletes, any benefit is usually modest and not guaranteed.

Safety and practical notes: oral L-glutamine supplements are generally well tolerated; mild gastrointestinal symptoms are the most commonly reported side effects. There are important precautions: people with severe liver disease, serious kidney disease, or certain metabolic disorders should consult a clinician before taking glutamine because it affects nitrogen and ammonia handling in the body. People with active cancer should also discuss glutamine with their oncologist — while glutamine can reduce some treatment side effects (like mucositis), the interaction between glutamine and tumor metabolism is complex and requires individualized medical advice. If you’re pregnant, breastfeeding, taking prescription medications, or have a chronic condition, talk to your healthcare provider before starting any supplement.

In short, L-glutamine is a biologically important amino acid with well-understood cellular roles that translate into real clinical benefits in situations of stress, illness, or tissue breakdown — especially for gut health, immune support during critical illness, and tissue repair. For everyday use by otherwise healthy people the benefits are far less certain. If you’re considering supplementation, a clinician or dietitian can help weigh the potential advantages against your personal health status and recommend an appropriate dose or form.

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Butyrate is a short-chain fatty acid made by gut bacteria when they ferment fiber. In the colon it is used as a fuel by the cells that line the gut, but it also travels into the circulation and acts as a signaling molecule. Those signaling actions are what scientists think help mitochondria — the tiny “power plants” inside cells — work better. (Box News)

One way butyrate helps mitochondria is by changing which genes are turned on or off. Butyrate is a natural inhibitor of enzymes called histone deacetylases (HDACs). By inhibiting HDACs, butyrate makes the cell’s gene-control machinery more permissive for certain key mitochondrial regulators, especially a protein called PGC-1α. PGC-1α is like a master switch for making more and better mitochondria: when its levels rise, cells increase mitochondrial biogenesis (they make more mitochondria) and turn on genes needed for energy production. This HDAC → PGC-1α route is one clear molecular path researchers have identified. (Diabetes Journals)

A second, closely related mechanism involves cellular energy sensors such as AMPK. Butyrate can activate AMPK, a sensor that turns on when a cell needs more energy. When AMPK is switched on it promotes mitochondrial biogenesis and improves mitochondrial quality control. In many experimental models, activation of AMPK by butyrate leads to stronger mitochondrial respiration, better fatty-acid burning, and an increase in proteins that help mitochondria work efficiently. Together with the PGC-1α effects, AMPK activation helps cells produce more ATP (usable energy) and use stored fat more effectively. (Frontiers)

Butyrate also helps maintain mitochondrial health by improving mitochondrial turnover — the balance between making new mitochondria and removing damaged ones. Studies show butyrate can promote mitophagy, the selective recycling of worn-out mitochondria, which lowers oxidative stress and prevents damaged mitochondria from harming the cell. Healthier mitochondria mean cells use oxygen more efficiently and produce fewer harmful reactive oxygen species, which supports better tissue function overall. (Wiley Online Library)

Finally, these molecular effects have practical consequences in whole-body metabolism. In animal experiments, butyrate treatment increases resting energy expenditure, encourages the “browning” of white fat (making fat cells more mitochondria-rich and heat-producing), and improves insulin sensitivity — all changes that depend on better mitochondrial function in muscle, fat, and other tissues. That is why researchers link butyrate’s mitochondrial effects to protection against diet-induced weight gain in rodents. However, most mechanistic work is in cells and animals; human trials are smaller and less conclusive, so we should be cautious about assuming identical effects in people. (Box News)

In short: butyrate helps mitochondria by altering gene regulation (HDAC inhibition → more PGC-1α), by activating energy sensors (AMPK), and by improving mitochondrial quality control (mitophagy). Those actions raise mitochondrial number and efficiency, lower damaging stress, and shift tissues toward burning more fuel — which together explain why butyrate is linked to improved metabolic health in experimental studies. At the same time, the strongest evidence so far comes from laboratory and animal work; translating this into reliable human therapies is an active area of research. (Diabetes Journals)

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Butyrate tightens the gut barrier through several complementary, fairly direct actions on the cells that line the intestine and on the local immune signals around them. First, colon cells use butyrate as a preferred fuel: when those cells burn butyrate for energy they have more ATP to maintain their normal activities, including making and holding together the proteins that seal the spaces between cells (the “tight junctions”). Butyrate also turns on cellular energy sensors such as AMP-activated protein kinase (AMPK), a pathway that helps maintain tight junction structure and promotes healthy cell metabolism.

Second, butyrate changes gene activity in epithelial cells by inhibiting histone deacetylases (HDACs). That biochemical effect relaxes chromatin and increases production of protective molecules: more mucin (the slippery gel that sits over the epithelium), more trefoil peptides that help repair the lining, and higher expression of tight-junction proteins (for example, claudins and occludin). Together these changes strengthen the physical mucus layer and the cellular seal, making the barrier less “leaky.”

Third, butyrate dampens local inflammation, and that matters for barrier integrity. It reduces production of pro-inflammatory cytokines and blunts activation of NF-κB, a master inflammatory switch. Less inflammation means less damage to the epithelium and less immune-driven opening of tight junctions. Butyrate also activates anti-inflammatory nuclear receptors like PPAR-γ and stimulates antimicrobial peptides, which help control microbes that would otherwise provoke inflammation.

Two important practical caveats follow from those mechanisms. One is concentration: at low, physiological levels butyrate supports cell growth, mucus production, and tight junction maintenance; at much higher concentrations it can trigger cell stress and apoptosis, which would harm the barrier. The other is location: most human butyrate is produced by bacterial fermentation of dietary fiber in the large intestine (colon). The small intestine naturally contains far lower butyrate levels because it has different microbes, faster transit, more oxygen, and less fiber fermentation. That means the clear, well-documented barrier benefits of butyrate apply most strongly in the colon. Producing the “same” protective effect in the small intestine typically requires either delivering butyrate directly to that region (for example with coated or pro-drug formulations that release butyrate downstream) or changing where bacteria produce short-chain fatty acids by altering the microbiota or the substrates they ferment (prebiotics, resistant starches, engineered probiotics, etc.).

In short, butyrate strengthens the gut barrier by supplying fuel, shifting gene expression toward protective proteins and mucus, and lowering damaging inflammation. Those actions are most effective in the large bowel where butyrate is naturally abundant; achieving comparable effects in the small bowel requires targeted delivery or deliberate changes to the microbial ecology so butyrate is produced locally at the right concentration.

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The key takeaway from this passage is that butyrate — a short-chain fatty acid made by gut bacteria — is a powerful protector of the gut. At physiologic (lower) concentrations it calms inflammation by turning down pro-inflammatory signals (for example IFN-γ, TNF-α, IL-1β, IL-6 and IL-8) and raising anti-inflammatory ones (like IL-10 and TGF-β), in part by blocking the inflammation master-switch NF-κB and activating anti-inflammatory receptors such as PPAR-γ. At the same time butyrate strengthens the physical defense of the intestine: it increases mucus (MUC2), boosts mucosal repair factors (trefoil factors), tightens junctions between cells, activates energy-sensing pathways (AMPK), and even stimulates antimicrobial peptides — all of which help keep pathogens and toxic molecules out of the body.

What makes this especially interesting is that butyrate’s effects are dose-dependent. Low, physiologic levels promote healthy cell growth and a tighter, less leaky barrier, while much higher concentrations can trigger cell death and damage the barrier. This explains why laboratory findings depend heavily on the butyrate concentrations used, and why doses used in treatments or in studies (for example, rectal doses used clinically) can differ from simple in-vitro experiments. In short, butyrate is both an anti-inflammatory signal and a barrier-builder in the gut, but its benefit hinges on the right amount and context.

(...) Short answer: mostly the large intestine (colon). Butyrate is produced and acts mainly in the colon, so its direct “leaky gut”–tightening effects are strongest there; effects in the small intestine are possible but less direct and less well-established. (PMC)

Explanation in plain language:

Butyrate is a food-made-by-your-gut-bacteria that your colon cells both eat and use as a signal. When colon cells burn butyrate for energy they stay healthy and happy, and that helps the layer of cells lining the gut stay intact. Butyrate also tells those cells to build stronger junctions between themselves — the microscopic “glue” that prevents leaks — by switching on cellular energy sensors (like AMPK) that speed up assembly of tight-junction proteins. This makes the barrier less leaky. (PMC)

Beyond tightening junctions, butyrate increases the production of mucus (the protective goo on the gut surface) and antimicrobial peptides, which together shield the epithelium from bacteria and toxins. It dampens inflammation by blocking inflammatory signaling pathways (for example NF-κB) and by changing gene activity through inhibition of histone deacetylases (HDACs), so the immune environment around the gut becomes less likely to damage the barrier. Those anti-inflammatory and mucous-boosting actions further reduce permeability. (ASM Journals)

One important caveat is dose and location: butyrate’s helpful effects are concentration-dependent — low, physiological levels strengthen the barrier, while much higher concentrations (seen only in some lab conditions) can cause cell stress or death. Also, because most butyrate is produced and used in the colon, the strongest and best-documented benefits are in the large intestine; getting the same effect in the small intestine usually requires different delivery or other changes to where bacteria produce short-chain fatty acids. (Nature)

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Laboratory and animal studies show neuroprotective actions for ashwagandha (Withania somnifera), and a handful of small human trials report modest cognitive benefits, but the clinical evidence is still preliminary and larger, longer studies are needed.

Researchers have studied ashwagandha for brain protection in two broad ways: first, by testing purified compounds from the plant (notably the withanolides such as withaferin A and related molecules) and second, by testing whole-root extracts in cells, animals and small human trials. In cell and animal experiments these compounds reduce oxidative stress and inflammation in brain tissue, help neurons resist toxic insults, and encourage processes that support neuron health such as neurite outgrowth and synaptic function. For example, several laboratory studies show that ashwagandha extracts can blunt the damage caused by beta-amyloid (a protein linked to Alzheimer’s disease), reduce markers of inflammation and cell death, and improve memory-related behavior in rodent models. These mechanistic and animal findings are summarized in recent reviews of the literature. (American Chemical Society)

How does it do that? The proposed mechanisms are familiar ones for a botanical with neuroprotective activity: antioxidant effects that lower harmful free radicals; anti-inflammatory actions that reduce damaging immune signaling in the brain; modulation of stress pathways (for example reducing excessive glucocorticoid/HPA-axis activation) that otherwise hurt neurons over time; and direct effects on protein handling and neuronal structure that can reduce toxic protein aggregation and support synapse formation. Specific chemicals from the plant — withanolides and sitoindosides — have been shown in lab work to engage these pathways, although which compound (or combination) matters for which effect is still being mapped out. (American Chemical Society)

What about human evidence? A handful of randomized, placebo-controlled trials have tested standardized root extracts in people. Some studies in stressed adults and in people with mild cognitive impairment report improved memory, attention and processing speed after several weeks to a few months of supplementation, and these trials generally reported good tolerability. However, the trials are small, used different extract preparations and doses, and often measured subjective or short-term endpoints — so while the results are encouraging, they do not yet prove that ashwagandha prevents or reverses major neurodegenerative diseases in people. Larger, longer and better-standardized clinical trials are underway or have been registered. (PubMed)

In plain terms: think of ashwagandha as a botanical that contains molecules able to protect nerve cells in laboratory settings and to nudge human cognition modestly in some small trials. That biological plausibility (antioxidant, anti-inflammatory, anti-amyloid and neurotrophic effects) makes it a promising candidate for further study, but the current human evidence is not yet strong enough to treat it as a proven therapy for Alzheimer’s, Parkinson’s or other major brain diseases. If you’re considering it for memory or brain health, it’s sensible to discuss it with a clinician — especially because product quality, dose and interactions vary. (PMC)

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