Tag: Molecule

  • Academia’s drug discovery challenges: Exploring the “publication landfill”

    Academia’s drug discovery challenges: Exploring the “publication landfill”

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    A new editorial paper was published in Oncotarget’s Volume 15 on January 24, 2024, entitled, “The fate of drug discovery in academia; dumping in the publication landfill?”

    In this new editorial, researchers Uzma Saqib, Isaac S. Demaree, Alexander G. Obukhov, Mirza S. Baig, Amiram Ariel, and Krishnan Hajela, from Devi Ahilya Vishwavidyalaya, Indore, discuss drug discovery-;a tedious process that is time consuming in both divulging whether a molecule is efficacious and specific in hitting the target and also in confirming that the potential drug does not cause severe adverse effects. Many drug candidates fail crossing multiple checkpoints of this long journey; they lag in one or several aspects and never move beyond the research bench to contribute to public health. These setbacks make the process of drug discovery very time consuming, expensive, and tedious. 

    “This viewpoint is focused on delineating how and why the multi-million [dollar] research efforts in the field of drug discovery often fail to reach its full potential.”

    There is no shortage of studies focusing on drug discovery. They are published on a daily basis describing the efforts encompassing conventional and/or modern drug discovery technology, including structure-based drug design (SBDD), virtual screening, high-throughput screening (HTS), Artificial Intelligence (AI), and cell-based screening approaches. However, many drug development strategies are rather fuzzy in their advancement. 

    Thus, there is a large gap between drug “discovery” and “development.” This part could be attributed to the lack of synergy between Academia and Industry at multiple levels. A significant part of this failure results from the lack of streamlining of drug development process. 

    “In the current perspective, we discussed why many therapeutic molecules never make it to clinical studies despite being proven efficacious pre-clinically. Additionally, we discussed the possible solutions to overcome this défaut of the drug development process.”

    Source:

    Journal reference:

    Saqib, U., et al. (2024). The fate of drug discovery in academia; dumping in the publication landfill? Oncotarget. doi.org/10.18632/oncotarget.28552.

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  • Paxlovid enhances treatment options for COVID-19 patients

    Paxlovid enhances treatment options for COVID-19 patients

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    In a recent review published in the Pharmaceutics, a group of authors explored the design, synthesis, and mechanism of action of Paxlovid, a Protease inhibitor (PI) drug combination for treating coronavirus disease 2019 (COVID-19).

    Study: The Design, Synthesis and Mechanism of Action of Paxlovid, a Protease Inhibitor Drug Combination for the Treatment of COVID-19. Image Credit: Tobias Arhelger/Shutterstock.com

    Background 

    The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, significantly challenged global healthcare systems and medical science.

    In response, researchers worldwide developed vaccines with innovative mechanisms and small-molecule antivirals targeting crucial viral proteins.

    Among these, PaxlovidTM, a blend of nirmatrelvir and ritonavir PIs, stands out for its effectiveness in treating COVID-19.

    Nirmatrelvir inhibits SARS-CoV-2’s main protease, vital for viral replication, while ritonavir boosts nirmatrelvir’s effectiveness by inhibiting Cytochrome P450 3A4 (CYP3A4), an enzyme that would otherwise degrade nirmatrelvir quickly.

    Further research is needed to develop alternative main protease (MPro) inhibitors despite the success of the nirmatrelvir-ritonavir combination, ensuring continued effectiveness against COVID-19.

    PIs as antivirals for Hepatitis C virus (HCV) and Human immunodeficiency virus (HIV) 

    PI Drugs for HCV and HIV Infections

    PIs are key in treating HCV and HIV infections. HCV, a small ribonucleic acid (RNA) virus causing hepatic diseases, is targeted by PIs like asunaporevir, telaprevir, and boceprevir, focusing on the nonstructural (NS)3/4A serine protease.

    These inhibitors are peptidomimetics, containing peptide bonds and a ‘warhead’ group that binds covalently but reversibly to the enzyme’s active site.

    HIV PIs target the virus’s aspartic acid protease, which is crucial for viral replication. They are used in antiretroviral therapy, transforming HIV from fatal to chronic.

    Development and mechanism of Nirmatrelvir

    Nirmatrelvir, developed from Pfizer’s earlier SARS-CoV-1 PI .. PF-00835231, faced challenges in oral absorption.

    Modifications like altering the warhead and substituting various molecular components enhanced its binding affinity and antiviral activity, eventually leading to nirmatrelvir with a nitrile warhead, improving solubility and synthesis.

    Despite different warheads, its structural similarity to boceprevir, and its role as a covalent inhibitor of SARS-CoV-2 Mpro makes it significant in COVID-19 treatment.

    Synthesis of nirmatrelvir

    Nirmatrelvir’s synthesis involves coupling the P1 building block and the P2-P3 dipeptide, with the final step being the formation of the nitrile warhead.

    The process starts with protected amino acid derivatives, proceeding through stages like Boc-deprotection, ester cleavage, and dipeptide formation.

    The synthesis yields nirmatrelvir with high efficiency and introduces a new approach involving a Ugi-type three-component reaction for higher diastereoselectivity.

    Synthesis and structure-activity relationship (SAR) study of nirmatrelvir analogs

    Research by Chia and co-workers led to the synthesizing nirmatrelvir analogs with different P1′ moieties, examining the role of the warhead in antiviral activity.

    These studies revealed varying levels of effectiveness in protease inhibition and antiviral activity, with some derivatives showing similar or superior effects to nirmatrelvir. However, challenges in cell penetration and specificity to SARS-CoV-2 limited the broader application of these analogs.

    Novel covalent and non-covalent inhibitors of SARS-CoV-2 Mpro

    Recent developments in SARS-CoV-2 Mpro inhibitors have introduced both peptidomimetic and non-peptidic inhibitors.

    These include warheads, such as epoxide rings and fluoromethyl groups, offering alternative mechanisms of covalent binding to the enzyme.

    Non-covalent inhibitors, like ensitrelvir, show lower reactivity but better selectivity due to their secondary interaction nature. These developments represent crucial steps in diversifying therapeutic options against COVID-19 and its evolving strains.

    Ritonavir as a pharmacokinetic enhancer

    Structure, activity, and interactions of ritonavir

    Originally an HIV protease inhibitor, Ritonavir is known for its efficacy at low doses (~100 mg) in inhibiting the CYP3A4 enzyme, a crucial element in drug metabolism.

    While high doses of Ritonavir are poorly tolerated, its low-dose effectiveness is leveraged in combination therapies with other HIV protease inhibitors, enhancing their half-lives and thus reducing required dosages.

    This unique use of Ritonavir has been explored even in early COVID-19 treatments. However, its use poses risks of significant drug–drug interactions, especially with medications metabolized by CYP3A4, potentially elevating their levels to toxic concentrations.

    Additionally, Ritonavir’s effect on other enzymes and transport proteins is noted, albeit of lesser importance in Paxlovid treatment.

    Synthesis of ritonavir

    developed at Abbott Laboratories, Ritonavir’s synthesis involves complex chemical processes, combining chiral amine and carboxylic acid building blocks.

    The synthesis starts with a cyclocondensation reaction involving thioformamide and ethyl 2-chloroacetate, followed by a series of steps leading to the formation of ritonavir.

    This intricate process involves various intermediate compounds and chemical reactions, including triethylamine and 4-dimethylaminopyridine, highlighting the sophistication required in pharmaceutical synthesis.

    The production of Ritonavir demonstrates the intricate chemical engineering necessary to develop effective pharmaceutical agents.

    Paxlovid—application and activity against mutant variants

    Paxlovid, combining nirmatrelvir and ritonavir, has shown significant efficacy in reducing COVID-19-related hospitalizations and mortality.

    While it has gained emergency use authorization in various regions, its effectiveness against emerging strains and mutant variants is under continuous scrutiny.

    The evolving landscape of SARS-CoV-2 mutations necessitates ongoing monitoring to ensure the sustained efficacy of treatments like Paxlovid.

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  • Small-molecule A485 mobilizes white blood cells on demand

    Small-molecule A485 mobilizes white blood cells on demand

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    White blood cells, or leukocytes, are the body’s first and second lines of defense against foreign organisms and particles. However, few drugs target these cells’ production and movement for clinically useful purposes. A new study published in the journal Immunity explores the signaling molecule landscape to identify potentially druggable targets for leukocyte migration into the bloodstream.

    Study: Small-molecule CBP/p300 histone acetyltransferase inhibition mobilizes leukocytes from the bone marrow via the endocrine stress response. Image Credit: Rost9 / ShutterstockStudy: Small-molecule CBP/p300 histone acetyltransferase inhibition mobilizes leukocytes from the bone marrow via the endocrine stress response. Image Credit: Rost9 / Shutterstock

    Leukocytes, including neutrophils, monocytes, and B lymphocytes, are formed in the bone marrow from blood-forming precursor cells and in a few other specialized organs. They are held in the bone marrow until they are released into the circulation. 

    There are two leukocyte compartments in the blood and peripheral tissues, which show changes in size with varying bodily states. For instance, when the body is injured, stressed, or infected, the number of leukocytes in the affected tissue alters and returns to normal once the threat is contained.

    Multiple regulatory steps take part in leukocyte breakdown as well as movement to different sites where they are needed. These originate in the central nervous system (CNS) in response to peripheral signals, being regulated by neural circuits in which both the sympathetic nervous system and the hypothalamo-pituitary-adrenal (HPA) axis participate.

    These signals work to increase bone marrow hemopoiesis, recruit leukocytes into the blood and other tissues where they are required, and ensure they return to normal levels once the challenge has been surmounted.

    In some disease conditions, this homeostatic control is lost, thus leading to abnormal counts, such as bone marrow failure on the one hand or acute leukemia on the other. As yet, though, few medications can help correct such dysregulation by modifying the rate of production, breakdown, or migration of leukocytes, whether in blood cancer, chronic inflammation, or acute hyperinflammatory states.

    Among available medications are the granulocyte colony-stimulating factor (G-CSF) family, CXC-motif chemokine receptor 4 (CXCR4) antagonists such as plerixafor/AMD3100), or inhibitors of the integrin very late antigen 4 (VLA4). G-CSF is, for instance, used to correct neutropenia in patients on chemotherapy but is less useful in patients with acute febrile conditions involving low neutrophil counts. Moreover, G-CSF can cause adverse effects in some patients.

    The need to know more about this field of pharmacology motivated the current study. It focuses on a small molecule called E1A-associated protein p300 (EP300 or p300), which is seen to be newly acquired during the leukemic phase of a condition called severe congenital neutropenia (SCN).

    The loss of function of this gene has led to reduced blood cell production if deleted before birth but high or leukemic leukocyte counts in later life. This has an ortholog, cyclic-adenosine-monophosphate-response-element-binding protein (CREBBP, also known as “CBP,” with 90% homology of sequence. One of the 8 domains in this gene is responsible for histone acetyltransferase (HAT) activity and contains a mutation in SCN that causes leukemic transformation.

    In this case, this domain might be druggable to produce “leukocytosis on demand” by altering the sizes of different leukocyte compartments.

    What did the study show?

    The scientists found that inhibiting the CBP/p300 domain with its HAT activity by the small molecule inhibitor A485 led to a reversible competitive inhibition of HAT enzyme activity, especially for CBP and p300 compared to other HATs. As expected, this led to a rapid rise in the levels of acetyl CoA within bone marrow macrophages in mouse models. The result was rapid leukocytosis.

    This was found to be a dose-dependent action and did not wane with repeated administration. When another type of CBP/p300 HAT inhibitor (C646) was used, the same effect was observed, confirming the mechanism of action. Conversely, inhibitors of DNA binding by the protein or of another HAT found in mammals failed to cause leukocytosis.

    A485 levels in the blood rapidly rose when injected into the mice, accumulating in bone marrow, adipose tissues, liver, spleen, and kidney, but not the brain. Leukocyte counts rose in parallel, including neutrophils, lymphocytes, and monocytes. A week later, no evidence of drug administration was observable, suggesting a transient effect.

    The rise in leukocyte counts was comparable with that achieved by G-CSF, though somewhat faster for neutrophils. When both were given, significantly higher neutrophil counts resulted. However, after 24 hours, all three blood cell types were raised with G-CSF vs A485.

    This indicates a shorter and different action of A485 compared to G-CSF.

    To extend the observations to human subjects, the researchers looked at data from a cohort of patients with a rare disease called Rubinstein-Taybi syndrome (RSTS), where CREBBP and EP300 mutations occur. About two-thirds had high leukocyte counts, with 70% showing mutations in the HAT domain. As expected, this group was more likely to show leukocytosis than the other group, where HAT was spared.

    Does this observation have clinical utility? To find out, they tested the effect of A485 in a cohort of mice with myelodysplastic syndrome (MDS), finding that the small molecule kept the leukocyte count normal. Secondly, they induced severe neutropenia by a course of chemotherapy in a mouse model, showing that A485 led to acute recovery of leukocyte counts.

    Then, they introduced the organism Listeria monocytogenes in a sepsis-inducing dose in mice with chemotherapy-induced pancytopenia. Neutrophils are vital to the immune defense against this microbe. After infection set in, they injected A485 vs. vehicle in controls.

    While those treated with the vehicle became sick and died of sepsis, A485 in a single dose led to improved survival, with fewer bacteria being recovered from treated animals. A485 mobilizes leukocytes from the bone marrow, which is the mechanism of leukocytosis. In contrast, there was no emergency hematopoiesis in the bone marrow.

    Different subsets of leukocytes responded to distinct pathways triggered by A485. These involve both G-CSF-dependent and –independent pathways of neutrophilia, but other pathways for lymphocytosis.

    Moreover, A485 uses neurohumoral pathways, specifically the HPA axis, to induce leukocytosis, as seen by the increased levels of glucocorticoids in the blood after A485 administration. The leukocytosis response triggered by the HPA activation does not rely on glucocorticoids, however, but occurs in response to CRHR1-regulated signals, including the adrenocorticotropic hormone (ACTH), that occurs with the loss of HPA feedback signals.

    While neutrophils increase with ACTH administration, lymphocyte counts increase only with glucocorticoid blockade, indicating that both are regulated differently.

    What are the implications?

    Competitive, reversible, small-molecule-mediated inhibition of the CBP/p300 HAT domain triggers acute and transient leukocyte mobilization from the bone marrow.” Further research is required to identify which clinical contexts are ideal for this drug. A485 may be better if only a rapid short increase in neutrophils is required, while long-term recovery of blood cell production in the bone marrow may call for G-CSF.

    The timing of administration for good results also needs to be defined since patients with neutropenic sepsis present at various time points and stages. Moreover, the value of such drugs in bacterial or viral, rather than listerial, sepsis remains unexplored.

    However, as reported by earlier researchers, it has anti-tumor effects, which could make it valuable in adjuvant therapy for cancer patients. The current study also sheds light on the role of ACTH, rather than its downstream products, glucocorticoids, on leukocyte homeostasis and G-CSF activity.

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  • CAR T cells target senescent cells, improve healthspan in mice

    CAR T cells target senescent cells, improve healthspan in mice

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    Chimeric antigen receptor (CAR) T cells have transformed the treatment of blood cancers in recent years. And there have been positive signs the “living drugs” can be harnessed against other diseases, like autoimmune disorders.

    Now laboratory research led by Memorial Sloan Kettering Cancer Center (MSK) and Cold Spring Harbor Laboratory suggests these engineered immune cells hold promise for treating some diseases related to aging, as well -; specifically, those caused by the accumulation of senescent cells (cells that stop dividing due to age or damage).

    An infusion of CAR T cells designed to target senescent cells was not only able to improve metabolic function in older mice and mice prematurely aged by a high-fat diet, but a single dose given to young, healthy mice also helped prevent metabolic decline later in life, according to findings the research team published in Nature Aging.

    When you hear ‘CAR T cell therapy,’ you think ‘cancer’ -; and it makes sense that it was pioneered at a place like MSK. But what we’re learning is that this approach of engineering immune cells to target disease has much broader possibilities.”


    Scott Lowe, PhD, senior study author, Chair of the Cancer Biology and Genetics Program in MSK’s Sloan Kettering Institute

    CAR T treatment improves metabolic function in mice

    In the study, younger mice were fed a high-fat diet for two months, which made them obese and caused metabolic stress. After an infusion of the experimental CAR T cells, the mice had lower body weight, better fasting blood glucose levels, and improved glucose and insulin tolerance, despite continuing the high-fat diet. They also had fewer senescent cells in the pancreas, liver, and fatty tissues than mice in a control group. Similar results were seen in older mice where metabolic function had decreased due to natural aging.

    Older mice that received the treatment even took longer to become exhausted when exercising. And the approach didn’t appear to cause any significant side effects.

    Further research is needed to see if the approach could extend the life span of the mice in addition to improving their “healthspan” -; that is, how long they stay healthy and free of disease, the scientists note.

    “We’re continuing to learn new things about senescence on a biological level,” Dr. Lowe says. “It will take time, but we’re interested in working with industry partners to move the laboratory findings into clinical trials.”

    There are a number of diseases associated with aging and chronic inflammation that potentially might be helped, Dr. Lowe says, such as chronic obstructive pulmonary disease (COPD), nonalcoholic steatohepatitis (NASH), osteoarthritis, metabolic syndrome, and even certain neurodegenerative diseases.

    Along with Dr. Lowe’s lab, immunologist Michel Sadelain, MD, PhD, and members of his lab were key collaborators in the research. Dr. Sadelain is a pioneer in the development of CAR T cell therapy, for which he was recently awarded the 2024 Breakthrough Prize in Life Sciences.

    The study was co-led by Inés Fernández-Maestre, a graduate student in the lab of MSK physician-scientist Ross Levine, MD, and by Corina Amor Vegas, MD, PhD, a former graduate student in the Lowe Lab who now heads her own lab at Cold Spring Harbor and is the corresponding author of the paper.

    Targeting senescent cells with CAR T

    A microscope image of an aged mouse liver showing signs of chronic inflammation (clusters of dark purple cells).

    Senescent cells are damaged cells that have gone into a protective, shutdown mode, where they stop dividing and actively send “help me” signals to the immune system. This can have some short-term benefits in contexts like wound healing and preventing the runaway cell division that happens in cancer, but it also can lead to chronic inflammation as senescent cells accumulate as people age.

    In 2020, researchers at MSK identified a molecule on the surface of senescent cells that was largely absent on other types of cells. This allowed them to design CAR T cells that could recognize and attack that specific molecule, called urokinase plasminogen activator receptor (uPAR). The team successfully tested the approach in several different mouse models of senescence-related diseases, including cancer and liver fibrosis, according to findings they published in Nature.

    The new research goes further in demonstrating that senolytic (senescence-targeting) cell therapies can improve symptoms associated with aging.

    The uPAR-targeting CAR T cells provide an alternative to the more traditional small-molecule drugs currently being investigated to clear senescent cells, notes Dr. Lowe, who is also a Howard Hughes Medical Institute Investigator.

    “One of the challenges with the current small-molecule drugs is that many don’t have a well-understood mechanism of action as it pertains to senescence. And a lot of them are repurposed cancer drugs with substantial toxicities.”

    Such drugs also must be given repeatedly.

    “T cells, however, have the ability to develop memory and persist in your body for really long periods, which is very different from a chemical drug,” notes Dr. Amor Vegas, who was also a co-first author on the earlier study. “With CAR T cells, you have the potential of getting this one treatment, and then that’s it. For chronic pathologies, that’s a huge advantage. Think about patients who need treatment multiple times per day versus you get an infusion, and then you’re good to go for multiple years.”

    Furthermore, with a cellular therapy, it’s possible to engineer in safety features to mitigate side effects as well as simultaneously to target multiple molecules on the surface of cells -; reducing the chances of them attacking healthy cells.

    Different challenges than using CAR T cell against cancer

    Through these experiments, the research team was able to show: uPAR-positive cells increase with age and significantly contribute to aging-related disfunction in tissues; uPAR-targeting CAR T cells can effectively eliminate the senescent cells without major side effects in mice; and that administering the treatment improved metabolism health in both normal aging and diet-related metabolic disease.

    Mice normally live about two years, and research found the uPAR-targeting CAR T cells persisted and expanded for more than 15 months in mice as they grew from youth into older age.

    “In some ways, using CAR T cells to treat age-associated diseases presents distinct challenges from using these therapies in cancer,” Dr. Lowe says. “If only a few cancer cells survive treatment, they may keep dividing to enable the tumor to relapse. Since senescent cells don’t divide, clearing most but not all of them should still produce substantial health benefits.”

    Still, there is a high safety bar for developing therapies for diseases that are less lethal than cancer.

    “We continue to develop new strategies to engineer cell therapies to be less toxic and less expensive,” Dr. Sadelain says. “These efforts will undoubtedly expand the list of diseases that can be treated by CAR T cell therapies in the coming years.”

    Source:

    Journal reference:

    Amor, C., et al. (2024). Prophylactic and long-lasting efficacy of senolytic CAR T cells against age-related metabolic dysfunction. Nature Aging. doi.org/10.1038/s43587-023-00560-5.

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