Exploring Holy Basil's Bioactive Compounds for T2DM Treatment: Docking and Molecular Dynamics Simulations with Human Omentin-1.

Type 2 Diabetes Mellitus (T2DM) presents a substantial health concern on a global scale, driving the search for innovative therapeutic strategies. Phytochemicals from medicinal plants, particularly Ocimum tenuiflorum (Holy Basil), have garnered attention for their potential in T2DM management. The increased focus on plant-based treatments stems from their perceived safety profile, lower risk of adverse effects, and the diverse range of bioactive molecules they offer, which can target multiple pathways involved in T2DM. Computational techniques explored the binding interactions between O. tenuiflorum phytochemicals and Human Omentin-1, a potential T2DM target. ADMET evaluation and targeted docking identified lead compounds: Luteolin (-4.84 kcal/mol), Madecassic acid (-4.12 kcal/mol), Ursolic acid (-5.91 kcal/mol), Stenocereol (-5.59 kcal/mol), and Apigenin (-4.64 kcal/mol), to have a better binding affinity to target protein compared to the control drug, Metformin (-2.01 kcal/mol). Subsequent molecular dynamics simulations evaluated the stability of Stenocereol, Luteolin, and Metformin complexes for 200 nanoseconds, analysing RMSD, RMSF, RG, SASA, PCA, FEL, and MM-PBSA parameters. Results indicated Stenocereol's strong binding affinity with Omentin-1, suggesting its potential as a potent therapeutic agent for T2DM management. These findings lay the groundwork for further experimental validation and drug discovery endeavours.

Genetic alteration of mRNA editing enzyme APOBEC3B in the pathogenesis of ovarian endometriosis.

RESEARCH QUESTION: What are the specific genetic alterations and associated network in endometriotic cells responsible for the disease pathogenesis? DESIGN: Case control experimental study involving 45 women with endometriosis who underwent laparoscopic surgery (case) and 45 normal samples from women undergoing total abdominal hysterectomy (control). The endometrial samples were subjected to whole exome sequencing (WES) of endometriotic tissue and copy number variation analysis. Validation of gene hits were obtained from WES using polymerase chain reaction techniques, immunological techniques, in-silico tools and transgenic cell line models. RESULTS: Germline heterozygous deletion of mRNA editing enzyme subunit APOBEC3B was identified in about 96% of endometriosis samples. The presence of germline deletion was confirmed with blood, endometrium and normal ovary samples obtained from the same patient. APOBEC3B deletions resulted in a hybrid protein that activates A1CF. APOBEC3B deletion can be a major cause of changes in the endometriotic microenvironment, and contributes to the pathogenesis and manifestation of the disease. The effect of APOBEC3B deletion was proved by in-vitro experiments in a cell line model, which displayed endometriosis-like characteristics. APOBEC3B germline deletion plays a major role in the pathogenesis of endometriosis, which is evident by the activation of A1CF, an increase in epithelial to mesenchymal transition, cellular proliferation, inflammation markers and a decrease in apoptosis markers. CONCLUSION: The deleterious effects caused by APOBEC3B deletion in endometriosis were identified and confirmed. These results might provide a base for identifying the complete pathogenetic mechanism of endometriosis, thereby moving a step closer to better diagnosis and treatment options.

Therapeutic potentials of glucose-dependent insulinotropic polypeptide (GIP) in T2DM: Past, present, and future.

Type 2 diabetes mellitus (T2DM) is a worldwide health problem that has raised major concerns to the public health community. This chronic condition typically results from the cell's inability to respond to normal insulin levels. Glucose-dependent insulinotropic polypeptide (GIP) and glucagon-like peptide-1 (GLP-1) are the primary incretin hormones secreted from the intestinal tract. While clinical research has extensively explored the therapeutic potential of GLP-1R in addressing various T2DM-related abnormalities, the possibility of GIPR playing an important role in T2DM treatment is still under investigation. Evidence suggests that GIP is involved in the pathophysiology of T2DM. This chapter focuses on examining the role of GIP as a therapeutic molecule in combating T2DM, comparing the past, present, and future scenarios. Our goal is to delve into how GIP may impact pancreatic ß-cell function, adipose tissue uptake, and lipid metabolism. Furthermore, we will elucidate the mechanistic functions of GIP and its receptors in relation to other clinical conditions like cardiovascular diseases, non-alcoholic fatty liver diseases, neurodegenerative diseases, and renal disorders. Additionally, this chapter will shed light on the latest advancements in pharmacological management for T2DM, highlighting potential structural modifications of GIP and the repurposing of drugs, while also addressing the challenges involved in bringing GIP-based treatments into clinical practice.

Hormonal regulation in diabetes: Special emphasis on sex hormones and metabolic traits.

Diabetes constitutes a significant global public health challenge that is rapidly reaching epidemic proportions. Among the non-communicable diseases, the incidence of diabetes is rising at an alarming rate. The International Diabetes Federation has documented a 9.09% prevalence of diabetes among individuals aged between 20 and 79 years. The interplay of gonadal hormones and gender differences is critical in regulating insulin sensitivity and glucose tolerance, and this dynamic is particularly crucial because of the escalating incidence of diabetes. Variations in insulin sensitivity are observed across genders, levels of adiposity, and age groups. Both estrogen and testosterone are seen to influence glucose metabolism and insulin sensitivity. This chapter surveys the present knowledge of sex differences, sex hormones, and chromosomes on insulin imbalance and diabetes development. It further highlights the influence of metabolic traits in diabetes and changes in sex hormones during diabetic pregnancy. Notably, even stressful lifestyles have been acknowledged to induce hormonal imbalances. Furthermore, it discusses the potential of hormonal therapy to help stabilize sex hormones in diabetic individuals and focuses on the most recent research investigating the correlation between sex hormones and diabetes.

Next-generation biomarkers for prognostic and potential therapeutic enhancement in Triple negative breast cancer.

Triple-negative breast carcinoma (TNBC) is one of the most challenging subtypes of breast carcinoma and it has very limited therapeutic options as it is highly aggressive. The prognostic biomarkers are crucial for early diagnosis of the tumor, it also helps in anticipating the trajectory of the illness and optimizing the therapy options. Several therapeutic biomarkers are being used. Among them, the next-generation biomarkers that include Circulating tumor (ct) DNA, glycogen, lipid, and exosome biomarkers provide intriguing opportunities for enhancing the prognosis of TNBC. Lipid and glycogen biomarkers serve as essential details on the development of the tumor along with the efficacy of the treatment, as it exhibits metabolic alteration linked to TNBC. Several types of biomarkers have predictive abilities in TNBC. Elevated levels are associated with worse outcomes. ctDNA being a noninvasive biomarker reveals the genetic composition of the tumor, as well as helps to monitor the progression of the disease. Traditional therapies are ineffective in TNBC due to a lack of receptors, targeted drug delivery provides a tailored approach to overcome drug resistance and site-specific action by minimizing the side effects in TNBC treatment. This enhances therapeutic outcomes against the aggressive nature of breast cancer. This paper includes all the recent biomarkers which has been researched so far in TNBC and the state of art for TNBC which is explored.

Molecular and cellular signalling pathways for promoting neural tissue growth - A tissue engineering approach.

Neural tissue engineering is a sub-field of tissue engineering that develops neural tissue. Damaged central and peripheral nervous tissue can be fabricated with a suitable scaffold printed with biomaterials. These scaffolds promote cell growth, development, and migration, yet they vary according to the biomaterial and scaffold printing technique, which determine the physical and biochemical properties. The physical and biochemical properties of scaffolds stimulate diverse signalling pathways, such as Wnt, NOTCH, Hedgehog, and ion channels- mediated pathways to promote neuron migration, elongation and migration. However, neurotransmitters like dopamine, acetylcholine, gamma amino butyric acid, and other signalling molecules are critical in neural tissue engineering to tissue fabrication. Thus, this review focuses on neural tissue regeneration with a tissue engineering approach highlighting the signalling pathways. Further, it explores the interaction of the scaffolds with the signalling pathways for generating neural tissue.

Expression of cell surface zinc transporter LIV1 in triple negative breast cancer is an indicator of poor prognosis and therapy failure.

Triple negative breast cancers (TNBC) are an aggressive molecular subtype of breast carcinoma (BC) identified by the lack of receptor expression for estrogen, progesterone, & human epidermal growth factor receptor-2. Lack of tangible drug targets warrants further research in TNBC. LIV1, is a zinc (Zn) transporter known to be overexpressed in few cancer types including BCs. Recently, in the United States of America, FDA approved the use of a new drug targeting LIV1, antibody drug conjugate SGN-LIV1A for treatment of TNBC patients. Though LIV1 also has a role in modulating immune cells by its differential transport of Zn, a correlation between the tumor cell expression of LIV1 and immune cell infiltrations were scantily reported. Further adequate baseline data on LIV1 expression in other populations have not been documented. Our objective was to screen a large Indian cohort of TNBC patient samples for LIV1, categorize the immune cell infiltration using CD4/CD8 expression and correlate the findings with therapy outcomes. Further, we also investigated for LIV1 expression in matched samples of primary & secondary tumors; pre & postchemotherapy in TNBC patients. Results showed an elevated expression of LIV1 in TNBC samples as compared to adjacent normal, the mean Q scores being 183.06 ± 6.39 and 120.78 ± 7.37 (p < 0.0001), respectively. Similarly, LIV1 levels were elevated in secondary tumors than primary & in patient samples postchemotherapy as compared to naïve. In the TNBC cohort, using automated method, cell morphology parameters were computed and analysis showed LIV1 levels were elevated in grade 3 TNBC samples presenting with altered cell morphology parameters namely cell size, cell perimeter, & nucleus size. Thus indicating LIV1 expressing TNBC samples portrayed an aggressive phenotype. Finally, TNBC patients with 3+ staining intensity showed poor survival (4.44 year) as compared to patients with 2+ LIV1 expression (5.47 year), emphasizing that LIV1 expression is a poor prognostic factor in TNBC. In conclusion, the study reports elevated expression of LIV1 in a large Indian TNBC cohort; high expression is a poor prognostic factor and correlated with aggressive disease and indicating the need for LIV1 targeted therapies.

Benzopyrene elimination from the environment using graphitic carbon nitride-SnS nanocomposites.

Benzopyrene (BaP) stands as a potent polycyclic aromatic hydrocarbon (PAH) molecule, boasting five fused aromatic rings, making its way into the human food chain through soil contamination. The persistent environmental presence of PAHs in soil, attributed to industrial exposure, is primarily due to their low molecular weight and hydrophobic nature. To preemptively address the entry of BaP into the food chain, the application of nanocomposites was identified as an effective remediation strategy. Post-synthesis, comprehensive characterization tests employing techniques such as UV-DRS, XRD, SEM-EDX, FTIR, and DLS unveiled the distinctive features of the g-C3N4-SnS nanocomposites. These nanocomposites exhibited spherical shapes embedded on layers of nanosheets, boasting particle diameters measuring 88.9 nm. Subsequent tests were conducted to assess the efficacy of eliminating benzopyrene from a combination of PAH molecules and g-C3N4-SnS nanocomposites. Varied parameters, including PAH concentration, adsorbent dosage, and suspension pH, were systematically explored. The optimized conditions for the efficient removal of BaP utilizing the g-C3N4-SnS nanocomposite involved 2 µg/mL of benzopyrene, 10 µg/mL of the nanocomposite, and a pH of 5, considering UV light as the irradiation source. The investigation into the mechanism governing BaP elimination closely aligned with batch adsorption results involved a thorough exploration of adsorption kinetics and isotherms. Photocatalytic degradation of benzopyrene was achieved, reaching a maximum of 86 % in 4 h and 36 % in 2 h, with g-C3N4-SnS nanocomposite acting as the catalyst. Further validation through HPLC data confirmed the successful removal of BaP from the soil matrix.

Current updates on metabolites and its interlinked pathways as biomarkers for diabetic kidney disease: A systematic review.

Diabetic kidney disease (DKD) is a major microvascular complication of diabetes mellitus (DM) that poses a serious risk as it can lead to end-stage renal disease (ESRD). DKD is linked to changes in the diversity, composition, and functionality of the microbiota present in the gastrointestinal tract. The interplay between the gut microbiota and the host organism is primarily facilitated by metabolites generated by microbial metabolic processes from both dietary substrates and endogenous host compounds. The production of numerous metabolites by the gut microbiota is a crucial factor in the pathogenesis of DKD. However, a comprehensive understanding of the precise mechanisms by which gut microbiota and its metabolites contribute to the onset and progression of DKD remains incomplete. This review will provide a summary of the current scenario of metabolites in DKD and the impact of these metabolites on DKD progression. We will discuss in detail the primary and gut-derived metabolites in DKD, and the mechanisms of the metabolites involved in DKD progression. Further, we will address the importance of metabolomics in helping identify potential DKD markers. Furthermore, the possible therapeutic interventions and research gaps will be highlighted.

Activation of oncogenic signaling kinase PAK1 by ionising radiation confers an aggressive phenotype in head and neck squamous cell carcinoma.

Head and neck squamous cancers are very aggressive tumors often diagnosed in late stages with poor prognosis. HNSCCs are usually treated by a course of radiation (IR) therapy and followed by surgery. These treatment regimens fail to bring a complete response. Molecular signatures in tumors are attributed to this response and an improved understanding of the signaling events could offer new avenues for therapy. Here, we show that P21 activated kinase-1 (PAK1) - an oncogenic signaling serine/threonine kinase, is activated upon exposure to IR and this leads to an accelerated tumorigenic character in HNSCC cells. Our results show that PAK1 is highly expressed in HNSCC cell lines, as compared to normal buccal mucosa cells and when HNSCC cells were exposed to IR, they show activated PAK1 and an aggressive phenotype as determined by in vitro functional assays. PAK1 levels were elevated in HNSCC as compared to adjacent normal oral tissues and our results also show convincing evidence of activated PAK1 in patient tumor samples of post- IR treatment as compared to pre-IR treatment and is associated with poor survival. Pak1 Knockout (KO) clones in HNSCC cells showed that they were more sensitive to IR as compared to wild type (wt) cells. This altered sensitivity to IR was attributed to enhanced DNA damage response modulated by PAK1 in cells. Overall, our results suggest that PAK1 expression in HNSCC could be a critical determinant in IR therapy response and silencing PAK1 is likely to be a treatment modality to improve clinical outcomes.

Sleep-associated insulin resistance promotes neurodegeneration.

Lifestyle modification can lead to numerous health issues closely associated with sleep. Sleep deprivation and disturbances significantly affect inflammation, immunity, neurodegeneration, cognitive depletion, memory impairment, neuroplasticity, and insulin resistance. Sleep significantly impacts brain and memory formation, toxin excretion, hormonal function, metabolism, and motor and cognitive functions. Sleep restriction associated with insulin resistance affects these functions by interfering with the insulin signalling pathway, neurotransmission, inflammatory pathways, and plasticity of neurons. So, in this review, We discuss the evidence that suggests that neurodegeneration occurs via sleep and is associated with insulin resistance, along with the insulin signalling pathways involved in neurodegeneration and neuroplasticity, while exploring the role of hormones in these conditions.

Environmental effects and interaction of nanoparticles on beneficial soil and aquatic microorganisms.

A steadily increasing production volume of nanoparticles reflects their numerous industrial and domestic applications. These economic successes come with the potential adverse effects on natural systems that are associated with their presence in the environment. Biological activities and effects of nanoparticles are affected by their entry method together with their specificities like their size, shape, charge, area, and chemical composition. Particles can be classified as safe or dangerous depending on their specific properties. As both aquatic and terrestrial systems suffer from organic and inorganic contamination, nanoparticles remain a sink for these contaminants. Researching the sources, synthesis, fate, and toxicity of nanoparticles has advanced significantly during the last ten years. We summarise nanoparticle pathways throughout the ecosystem and their interactions with beneficial microorganisms in this research. The prevalence of nanoparticles in the ecosystem causes beneficial microorganisms to become hazardous to their cells, which prevents the synthesis of bioactive molecules from undergoing molecular modifications and diminishes the microbe population. Recently, observed concentrations in the field could support predictions of ambient concentrations based on modeling methodologies. The aim is to illustrate the beneficial and negative effects that nanoparticles have on aqueous and terrestrial ecosystems, as well as the methods utilized to reduce their toxicity.

Deregulated Metabolic Pathways in Ovarian Cancer: Cause and Consequence.

Ovarian cancers are tumors that originate from the different cells of the ovary and account for almost 4% of all the cancers in women globally. More than 30 types of tumors have been identified based on the cellular origins. Epithelial ovarian cancer (EOC) is the most common and lethal type of ovarian cancer which can be further divided into high-grade serous, low-grade serous, endometrioid, clear cell, and mucinous carcinoma. Ovarian carcinogenesis has been long attributed to endometriosis which is a chronic inflammation of the reproductive tract leading to progressive accumulation of mutations. Due to the advent of multi-omics datasets, the consequences of somatic mutations and their role in altered tumor metabolism has been well elucidated. Several oncogenes and tumor suppressor genes have been implicated in the progression of ovarian cancer. In this review, we highlight the genetic alterations undergone by the key oncogenes and tumor suppressor genes responsible for the development of ovarian cancer. We also summarize the role of these oncogenes and tumor suppressor genes and their association with a deregulated network of fatty acid, glycolysis, tricarboxylic acid and amino acid metabolism in ovarian cancers. Identification of genomic and metabolic circuits will be useful in clinical stratification of patients with complex etiologies and in identifying drug targets for personalized therapies against cancer.

Novel BH4-BCL-2 Domain Antagonists Induce BCL-2-Mediated Apoptosis in Triple-Negative Breast Cancer.

Targeting the challenging tumors lacking explicit markers and predictors for chemosensitivity is one of the major impediments of the current cancer armamentarium. Triple-negative breast cancer (TNBC) is an aggressive and challenging molecular subtype of breast cancer, which needs astute strategies to achieve clinical success. The pro-survival B-cell lymphoma 2 (BCL-2) overexpression reported in TNBC plays a central role in deterring apoptosis and is a promising target. Here, we propose three novel BH4 mimetic small molecules, SM396, a covalent binder, and two non-covalent binders, i.e., SM216 and SM949, which show high binding affinity (nM) and selectivity, designed by remodeling the existing BCL-2 chemical space. Our mechanistic studies validate the selectivity of the compounds towards cancerous cells and not on normal cells. A series of functional assays illustrated BCL-2-mediated apoptosis in the tumor cells as a potent anti-cancerous mechanism. Moreover, the compounds exhibited efficacious in vivo activity as single agents in the MDA-MB-231 xenograft model (at nanomolar dosage). Overall, these findings depict SM216, SM396, and SM949 as promising leads, pointing to the clinical translation of these compounds in targeting triple-negative breast cancer.

Zinc transporter LIV1: A promising cell surface target for triple negative breast cancer.

Breast cancer is one of the leading causes contributing to the global cancer burden. The triple negative breast cancer (TNBC) molecular subtype accounts for the most aggressive type. Despite progression in therapeutic options and prognosis in breast cancer treatment options, there remains a high rate of distant relapse. With advancements in understanding the role of zinc and zinc carriers in the prognosis and treatment of the disease, the scope of precision treatment/targeted therapy has been expanded. Zinc levels and zinc transporters play a vital role in maintaining cellular homeostasis, tumor surveillance, apoptosis, and immune function. This review focuses on the zinc transporter, LIV1, as an essential target for breast cancer prognosis and emerging treatment options. Previous studies give an insight into the role of LIV1 in fulfilling the most important hallmarks of cancer such as apoptosis, metastasis, invasion, and evading the immune system. Normal tissue expression of LIV1 is limited. Higher expression of LIV1 has been linked to Epithelial-Mesenchymal Transition, histological grade of cancer, and early node metastasis. LIV1 was found to be one of the attractive targets in the therapeutic hunt for TNBCs. TNBCs are an immunogenic breast cancer subtype. As zinc transporters are known to serve as the metabolic gatekeepers of immune cells, this review bridges tumor infiltrating lymphocytes, TNBC and LIV1. In addition, the suitability of LIV1 as an antibody-drug conjugate (Seattle genetics [SGN]-LIV1A) target in TNBC, represents a promising strategy for patients. Early clinical trial results reveal that this novel agent reduces tumor burden by inducing mitotic arrest, immunomodulation, and immunogenic cell death, warranting further investigation of SGN-LIV1A in combination with immuno-oncology agents. Priming the patient's immune response in combination with SGN-LIV1A could eventually change the landscape for the TNBC patient population.

HMGB3 inhibition by miR-142-3p/sh-RNA modulates autophagy and induces apoptosis via ROS accumulation and mitochondrial dysfunction and reduces the tumorigenic potential of human breast cancer cells.

AIMS: High mobility group box (HMGB) family proteins, HMGB1, HMGB2, HMGB3, and HMGB4 are oncogenic. The oncogenic nature of HMGB1 is characterized by its association with autophagy, ROS, and MMP. Since HMGB3 is its paralog, we hypothesized that it might also modulate autophagy, ROS, and MMP. Hence, we targeted HMGB3 using its shRNA or miR-142-3p and assessed the changes in autophagy, ROS, MMP, and tumorigenic properties of human breast cancer cells. MAIN METHODS: Cell viability was assessed by resazurin staining and annexin-V/PI dual staining was used for confirming apoptosis. Colony formation, transwell migration, invasion and luciferase reporter (for miRNA-target validation) assays were also performed. ROS and MMP were detected using DHE and MitoTracker dyes, respectively. A zebrafish xenograft model was used to assess the role of miR-142-3p on in vivo metastatic potential of breast cancer cells. KEY FINDINGS: Breast cancer tissues from Indian patients and TCGA samples exhibit overexpression of HMGB3. miR-142-3p binds to 3' UTR of HMGB3, leading to its downregulation that subsequently inhibits colony formation and induces apoptosis involving increased ROS accumulation and decreased MMP, phospho-mTOR and STAT3. Our findings show that HMGB3 is directly involved in the miR-142-3p-mediated disruption of autophagy and induction of apoptotic cell death via modulation of LC3, cleaved PARP and Bcl-xL. In addition, miR-142-3p inhibited migration, invasion and metastatic potential of breast cancer cells. SIGNIFICANCE: Our findings highlighted the role of HMGB3, for the first time, in the modulation of autophagy and apoptosis in human breast cancer cells, and these results have therapeutic implications.

p21 activated kinase-1 and tamoxifen - A deadly nexus impacting breast cancer outcomes.

Tamoxifen is a commonly used drug in the treatment of ER + ve breast cancers since 1970. However, development of resistance towards tamoxifen limits its remarkable clinical success. In this review, we have attempted to provide a brief overview of multiple mechanism that may lead to tamoxifen resistance, with a special emphasis on the roles played by the oncogenic kinase- PAK1. Analysing the genomic data sets available in the cBioPortal, we found that PAK1 gene amplification significantly affects the Relapse Free Survival of the ER + ve breast cancer patients. While PAK1 is known to promote tamoxifen resistance by phosphorylating ERα at Ser305, existing literature suggests that PAK1 can fuel up tamoxifen resistance obliquely by phosphorylating other substrates. We have summarised some of the approaches in the mass spectrometry based proteomics, which would enable us to study the tamoxifen resistance specific phosphoproteomic landscape of PAK1. We also propose that elucidating the multiple mechanisms by which PAK1 promotes tamoxifen resistance might help us discover druggable targets and biomarkers.

Inflammation-induced PELP1 expression promotes tumorigenesis by activating GM-CSF paracrine secretion in the tumor microenvironment.

The inflammatory tumor microenvironment has been implicated as a major player fueling tumor progression and an enabling characteristic of cancer, proline, glutamic acid, and leucine-rich protein 1 (PELP1) is a novel nuclear receptor coregulator that signals across diverse signaling networks, and its expression is altered in several cancers. However, investigations to find the role of PELP1 in inflammation-driven oncogenesis are limited. Molecular studies here, utilizing macrophage cell lines and animal models upon stimulation with lipopolysaccharide (LPS) or necrotic cells, showed that PELP1 is an inflammation-inducible gene. Studies on the PELP1 promoter and its mutant identified potential binding of c-Rel, an NF-κB transcription factor subunit, to PELP1 promoter upon LPS stimulation in macrophages. Recruitment of c-Rel onto the PELP1 promoter was validated by chromatin immunoprecipitation, further confirming LPS mediated PELP1 expression through c-Rel-specific transcriptional regulation. Macrophages that overexpress PELP1 induces granulocyte-macrophage colony-stimulating factor secretion, which mediates cancer progression in a paracrine manner. Results from preclinical studies with normal-inflammatory-tumor progression models demonstrated a progressive increase in the PELP1 expression, supporting this link between inflammation and cancer. In addition, animal studies demonstrated the connection of PELP1 in inflammation-directed cancer progression. Taken together, our findings provide the first report on c-Rel-specific transcriptional regulation of PELP1 in inflammation and possible granulocyte-macrophage colony-stimulating factor-mediated transformation potential of activated macrophages on epithelial cells in the inflammatory tumor microenvironment, reiterating the link between PELP1 and inflammation-induced oncogenesis. Understanding the regulatory mechanisms of PELP1 may help in designing better therapeutics to cure various inflammation-associated malignancies.

Water Mapping and Scoring Approaches to Predict the Role of Hydration Sites in the Binding Affinity of PAK1 Inhibitors.

AIM: This study aims to develop and establish a computational model that can identify potent molecules for p21-activating kinase 1 (PAK1) Background: PAK1 is a well-established drug target that has been explored for various therapeutic interventions. Control of this protein requires an indispensable inhibitor to curb the structural changes and subsequent activation of signalling effectors responsible for the progression of diseases, such as cancer, inflammatory, viral, and neurological disorders. OBJECTIVE: The study aims to establish a computational model that could identify active molecules which will further provide a platform for developing potential PAK1 inhibitors. METHODS: A congeneric series of 27 compounds were considered for this study, with Ki (nm) covering a minimum of 3 log range. The compounds were developed based on a previously reported Group-I PAK inhibitor, namely G-5555. The 27 compounds were subjected to the SP and XP mode of docking to understand the binding mode, its conformation and interaction patterns. To understand the relevance of biological activity from computational approaches, the compounds were scored against generated water maps to obtain WM/MM ΔG binding energy. Moreover, molecular dynamics analysis was performed for the highly active compound to understand the conformational variability and stability of the complex. We then evaluated the predictable binding pose obtained from the docking studies. RESULTS: From the SP and XP modes of docking, the common interaction pattern with the amino acid residues Arg299 (cation-π), Glu345 (Aromatic hydrogen bond), hinge region Leu347, salt bridges Asp393 and Asp407 was observed, among the congeneric compounds. The interaction pattern was compared with the co-crystal inhibitor FRAX597 of the PAK1 crystal structure (PDB id: 4EQC). The correlation with different docking parameters in the SP and XP modes was insignificant and thereby revealed that the SP and XP's scoring functions could not predict the active compounds. This was due to the limitations in the docking methodology that neglected the receptor flexibility and desolvation parameters. Hence, to recognise the desolvation and explicit solvent effects, as well as to study the Structure-Activity Relationships (SARs) extensively, WaterMap (WM) calculations were performed on the congeneric compounds. Based on displaceable unfavourable hydration sites (HS) and their associated thermodynamic properties, the WM calculations facilitated in understanding the significance of correlation in the folds of activity of highly active (19 and 17), moderately active (16 and 21) and less active (26 and 25) compounds. Furthermore, the scoring function from WaterMap, namely WM/MM, led to a significant R2 value of 0.72 due to a coupled conjunction with MM treatment and displaced unfavourable waters at the binding site. To check the "optimal binding conformation", molecular dynamics simulation was carried out with the highly active compound 19 to explain the binding mode, stability, interactions, solvent-accessible area, etc., which could support the predicted conformation with bioactive conformation. CONCLUSION: This study determined the best scoring function, established SARs and predicted active molecules through a computational model. This will contribute to the development of the most potent PAK1 inhibitors.

WaterMap and Molecular Dynamic Simulation-Guided Discovery of Potential PAK1 Inhibitors Using Repurposing Approaches.

p21-Activated kinase 1 (PAK1) is positioned at the nexus of several oncogenic signaling pathways. Currently, there are no approved inhibitors for disabling the transfer of phosphate in the active site directly, as they are limited by lower affinity, and poor kinase selectivity. In this work, a repurposing study utilizing FDA-approved drugs from the DrugBank database was pursued with an initial selection of 27 molecules out of ∼2162 drug molecules, based on their docking energies and molecular interaction patterns. From the molecules that were considered for WaterMap analysis, seven molecules, namely, Mitoxantrone, Labetalol, Acalabrutinib, Sacubitril, Flubendazole, Trazodone, and Niraparib, ascertained the ability to overlap with high-energy hydration sites. Considering many other displaced unfavorable water molecules, only Acalabrutinib, Flubendazole, and Trazodone molecules highlighted their prominence in terms of binding affinity gains through ΔΔG that ranges between 6.44 and 2.59 kcal/mol. Even if Mitoxantrone exhibited the highest docking score and greater interaction strength, it did not comply with the WaterMap and molecular dynamics simulation results. Moreover, detailed MD simulation trajectory analyses suggested that the drug molecules Flubendazole, Niraparib, and Acalabrutinib were highly stable, observed from their RMSD values and consistent interaction pattern with Glu315, Glu345, Leu347, and Asp407 including the hydrophobic interactions maintained in the three replicates. However, the drug molecule Trazodone displayed a loss of crucial interaction with Leu347, which was essential to inhibit the kinase activity of PAK1. The molecular orbital and electrostatic potential analyses elucidated the reactivity and strong complementarity potentials of the drug molecules in the binding pocket of PAK1. Therefore, the CADD-based reposition efforts, reported in this work, helped in the successful identification of new PAK1 inhibitors that requires further investigation by in vitro analysis.