Miracle-dz/UniFAR-FTUs huggingface dataset:
Heterocyclic Substitutions Greatly Improve Affinity and Stability of Folic Acid towards FRα. an In Silico Insight

Folate receptor alpha (FRα) is known as a biological marker for many cancers due to its overexpression in cancerous epithelial tissue. The folic acid (FA) binding affinity to the FRα active site provides a basis for designing more specific targets for FRα. Heterocyclic rings have been shown to interact with many receptors and are important to the metabolism and biological processes within the body. Nineteen FA analogs with substitution with various heterocyclic rings were designed to have higher affinity toward FRα. Molecular docking was used to study the binding affinity of designed analogs compared to FA, methotrexate (MTX), and pemetrexed (PTX). Out of 19 FA analogs, analogs with a tetrazole ring (FOL03) and benzothiophene ring (FOL08) showed the most negative binding energy and were able to interact with ASP81 and SER174 through hydrogen bonds and hydrophobic interactions with amino acids of the active site. Hence, 100 ns molecular dynamics (MD) simulations were carried out for FOL03, FOL08 compared to FA, MTX, and PTX. The root mean square deviation (RMSD) and root mean square fluctuation (RMSF) of FOL03 and FOL08 showed an apparent convergence similar to that of FA, and both of them entered the binding pocket (active site) from the pteridine part, while the glutamic part was stuck at the FRα pocket entrance during the MD simulations. Molecular mechanics Poisson-Boltzmann surface accessible (MM-PBSA) and H-bond analysis revealed that FOL03 and FOL08 created more negative free binding and electrostatic energy compared to FA and PTX, and both formed stronger H-bond interactions with ASP81 than FA with excellent H-bond profiles that led them to become bound tightly in the pocket. In addition, pocket volume calculations showed that the volumes of active site for FOL03 and FOL08 inside the FRα pocket were smaller than the FA–FRα system, indicating strong interactions between the protein active site residues with these new FA analogs compared to FA during the MD simulations.
Pharmacological Potential of Fungal Endophytes Associated with Medicinal Plants: A Review

Endophytic microbes are microorganisms that colonize the intracellular spaces within the plant tissues without exerting any adverse or pathological effects. Currently, the world population is facing devastating chronic diseases that affect humans. The resistance of pathogens to commercial antibiotics is increasing, thus limiting the therapeutic potential and effectiveness of antibiotics. Consequently, the need to search for novel, affordable and nontoxic natural bioactive compounds from endophytic fungi in developing new drugs with multifunction mechanisms to meet human needs is essential. Fungal endophytes produce invaluable bioactive metabolic compounds beneficial to humans with antimicrobial, anticancer, antidiabetic, anti-inflammatory, antitumor properties, etc. Some of these bioactive compounds include pestacin, taxol, camptothecin, ergoflavin, podophyllotoxin, benzopyran, isopestacin, phloroglucinol, tetrahydroxy-1-methylxanthone, salidroside, borneol, dibenzofurane, methyl peniphenone, lipopeptide, peniphenone etc. Despite the aforementioned importance of endophytic fungal metabolites, less information is available on their exploration and pharmacological importance. Therefore, in this review, we shall elucidate the fungal bioactive metabolites from medicinal plants and their pharmacological potential.
Krüppel-like factor 4 promotes survival and expansion in acute myeloid leukemia cells

Acute myeloid leukemia (AML) is an aggressive hematological malignancy of the bone marrow that affects mostly elderly adults. Alternative therapies are needed for AML patients because the overall prognosis with current standard of care, high dose chemotherapy and allogeneic transplantation, remains poor due to the emergence of refractory and relapsed disease. Here, we found expression of the transcription factor KLF4 in AML cell lines is not silenced through KLF4 gene methylation nor via proteasomal degradation. The deletion of KLF4 by CRISPR-CAS9 technology reduced cell growth and increased apoptosis in both NB4 and MonoMac-6 cell lines. Chemical induced differentiation of gene edited NB4 and MonoMac6 cells with ATRA and PMA respectively increased apoptosis and altered expression of differentiating markers CD11b and CD14. Transplantation of NB4 and MonoMac-6 cells lacking KLF4 into NSG mice resulted in improved overall survival compared to the transplantation of parental cell lines. Finally, loss-of-KLF4 did not alter sensitivity of leukemic cells to the chemotherapeutic drugs daunorubicin and cytarabine. These results suggest that KLF4 expression supports AML cell growth and survival, and the identification and disruption of KLF4-regulated pathways could represent an adjuvant therapeutic approach to increase response.
Pneumocystis Pneumonia: Immunity, Vaccines, and Treatments

For individuals who are immunocompromised, the opportunistic fungal pathogen Pneumocystis jirovecii is capable of causing life-threatening pneumonia as the causative agent of Pneumocystis pneumonia (PCP). PCP remains an acquired immunodeficiency disease (AIDS)-defining illness in the era of antiretroviral therapy. In addition, a rise in non-human immunodeficiency virus (HIV)-associated PCP has been observed due to increased usage of immunosuppressive and immunomodulating therapies. With the persistence of HIV-related PCP cases and associated morbidity and mortality, as well as difficult to diagnose non-HIV-related PCP cases, an improvement over current treatment and prevention standards is warranted. Current therapeutic strategies have primarily focused on the administration of trimethoprim-sulfamethoxazole, which is effective at disease prevention. However, current treatments are inadequate for treatment of PCP and prevention of PCP-related death, as evidenced by consistently high mortality rates for those hospitalized with PCP. There are no vaccines in clinical trials for the prevention of PCP, and significant obstacles exist that have slowed development, including host range specificity, and the inability to culture Pneumocystis spp. in vitro. In this review, we overview the immune response to Pneumocystis spp. , and discuss current progress on novel vaccines and therapies currently in the preclinical and clinical pipeline.
Coronavirus Disease 2019 (COVID-19) Epidemic and Mental Health Status in the General Adult Population of Serbia: A Cross-Sectional Study

Since its outbreak, coronavirus disease 2019 (COVID-19) has rapidly spread throughout the world. The Serbian government declared a state of emergency on 15 March 2020, implementing some of Europe’s strictest measures to combat the pandemic. The aim of this study was to determine the impact of the COVID-19 epidemic on the mental health of the general adult Serbian population and to identify associated factors during the state of emergency and lockdown. Data were collected with a snowball sampling method between 23 March and 25 April 2020, by using an online questionnaire. Multiple ordinal regression was performed to establish the associations between socio-demographic characteristics, self-estimated health status, and depression, anxiety, and stress. Out of 1057 participants included in the study, 28.9%, 36.9%, and 38.1% reported moderate to severe depression, anxiety, and stress symptoms. Uneasiness related to COVID-19 news, the feeling of helplessness, likeliness of impending death, and presence of COVID-19 symptoms were associated with higher depression, anxiety, and stress scores. Current smoking status was associated with a higher risk of depression and stress. Students had a significantly higher level of depression and stress, while older age was protective against anxiety and stress. Higher socioeconomic status was significantly associated with lower levels of depression, anxiety, and stress.
Primary Effusion Lymphoma: A Clinicopathological Study of 70 Cases

Simple Summary Primary effusion lymphoma (PEL) is a rare HHV8 driven large B-cell lymphoma. It is often associated with HIV infection and seldom occurs in HIV-negative immunocompromised patients. Patients with PEL usually present with effusion only, but occasionally with an extracavitary mass, or both. This retrospective study aimed to better characterize the clinicopathological features of PEL by comparing effusion-only PEL versus the extracavitary-only PEL and HIV-positive versus HIV-negative cases in a large cohort of 70 patients. All 70 (100%) cases were positive for HHV8. Fifty-six (80%) patients had HIV infection. Patients presenting with effusion only versus extracavitary disease were associated with different clinicopathologic features. After a median follow-up time of 40 months (range 0–96), 26 of 52 (50%) patients with clinical follow-up died, and the median survival was 42.5 months. PEL is an aggressive lymphoma with a poor prognosis, regardless of extracavitary presentation or HIV status. Abstract Primary effusion lymphoma (PEL) is a rare type of large B-cell lymphoma associated with human herpesvirus 8 (HHV8) infection. Patients with PEL usually present with an effusion, but occasionally with an extracavitary mass. In this study, we reported a cohort of 70 patients with PEL: 67 men and 3 women with a median age of 46 years (range 26–91). Of these, 56 (80%) patients had human immunodeficiency virus (HIV) infection, eight were HIV-negative, and six had unknown HIV status. Nineteen (27%) patients had Kaposi sarcoma. Thirty-five (50%) patients presented with effusion only, 27 (39%) had an extracavitary mass or masses only, and eight (11%) had both effusion and extracavitary disease. The lymphoma cells showed plasmablastic, immunoblastic, or anaplastic morphology. All 70 (100%) cases were positive for HHV8. Compared with effusion-only PEL, patients with extracavitary-only PEL were younger (median age, 42 vs. 52 years, p = 0.001), more likely to be HIV-positive (88.9% vs. 68.6%, p = 0.06) and EBV-positive (76.9% vs. 51.9%, p = 0.06), and less often positive for CD45 (69.2% vs. 96.2%, p = 0.01), EMA (26.7% vs. 100%, p = 0.0005), and CD30 (60% vs. 81.5%, p = 0.09). Of 52 (50%) patients with clinical follow-up, 26 died after a median follow-up time of 40.0 months (range 0–96), and the median overall survival was 42.5 months. The median OS for patients with effusion-only and with extracavitary-only PEL were 30.0 and 37.9 months, respectively (p = 0.34), and patients with extracavitary-only PEL had a lower mortality rate at the time of last follow-up (35% vs. 61.5%, p = 0.07). The median OS for HIV-positive and HIV-negative patients were 42.5 and 6.8 months, respectively (p = 0.57), and they had a similar mortality rate of 50% at last follow-up. In conclusion, patients presenting with effusion-only versus extracavitary-only disease are associated with different clinicopathologic features. PEL is an aggressive lymphoma with a poor prognosis, regardless of extracavitary presentation or HIV status.
Interpersonal Motor Interactions Shape Multisensory Representations of the Peripersonal Space

This perspective review focuses on the proposal that predictive multisensory integration occurring in one’s peripersonal space (PPS) supports individuals’ ability to efficiently interact with others, and that integrating sensorimotor signals from the interacting partners leads to the emergence of a shared representation of the PPS. To support this proposal, we first introduce the features of body and PPS representations that are relevant for interpersonal motor interactions. Then, we highlight the role of action planning and execution on the dynamic expansion of the PPS. We continue by presenting evidence of PPS modulations after tool use and review studies suggesting that PPS expansions may be accounted for by Bayesian sensory filtering through predictive coding. In the central section, we describe how this conceptual framework can be used to explain the mechanisms through which the PPS may be modulated by the actions of our interaction partner, in order to facilitate interpersonal coordination. Last, we discuss how this proposal may support recent evidence concerning PPS rigidity in Autism Spectrum Disorder (ASD) and its possible relationship with ASD individuals’ difficulties during interpersonal coordination. Future studies will need to clarify the mechanisms and neural underpinning of these dynamic, interpersonal modulations of the PPS.
LOXL2 Inhibitors and Breast Cancer Progression

LOX (lysyl oxidase) and lysyl oxidase like-1–4 (LOXL 1–4) are amine oxidases, which catalyze cross-linking reactions of elastin and collagen in the connective tissue. These amine oxidases also allow the cross-link of collagen and elastin in the extracellular matrix of tumors, facilitating the process of cell migration and the formation of metastases. LOXL2 is of particular interest in cancer biology as it is highly expressed in some tumors. This protein also promotes oncogenic transformation and affects the proliferation of breast cancer cells. LOX and LOXL2 inhibition have thus been suggested as a promising strategy to prevent metastasis and invasion of breast cancer. BAPN (β-aminopropionitrile) was the first compound described as a LOX inhibitor and was obtained from a natural source. However, novel synthetic compounds that act as LOX/LOXL2 selective inhibitors or as dual LOX/LOX-L inhibitors have been recently developed. In this review, we describe LOX enzymes and their role in promoting cancer development and metastases, with a special focus on LOXL2 and breast cancer progression. Moreover, the recent advances in the development of LOXL2 inhibitors are also addressed. Overall, this work contextualizes and explores the importance of LOXL2 inhibition as a promising novel complementary and effective therapeutic approach for breast cancer treatment.
Assessment of Disability Progression Independent of Relapse and Brain MRI Activity in Patients with Multiple Sclerosis in Poland

The aim of the study was to verify the association of clinical relapses and brain activity with disability progression in relapsing/remitting multiple sclerosis patients receiving disease-modifying treatments in Poland. Disability progression was defined as relapse-associated worsening (RAW), progression independent of relapse activity (PIRA), and progression independent of relapses and brain MRI Activity (PIRMA). Data from the Therapeutic Program Monitoring System were analyzed. Three panels of patients were identified: R0, no relapse during treatment, and R1 and R2 with the occurrence of relapse during the first and the second year of treatment, respectively. In the R0 panel, we detected 4.6% PIRA patients at 24 months (p < 0.001, 5.0% at 36 months, 5.6% at 48 months, 6.1% at 60 months). When restricting this panel to patients without brain MRI activity, we detected 3.0% PIRMA patients at 12 months, 4.5% at 24 months, and varying from 5.3% to 6.2% between 36 and 60 months of treatment, respectively. In the R1 panel, RAW was detected in 15.6% patients at 12 months and, in the absence of further relapses, 9.7% at 24 months and 6.8% at 36 months of treatment. The R2 group was associated with RAW significantly more frequently at 24 months compared to the R1 at 12 months (20.7%; p < 0.05), but without a statistical difference later on. In our work, we confirmed that disability progression was independent of relapses and brain MRI activity.
MicroRNA-429 acts as a tumor suppressor in colorectal cancer by targeting high mobility group box 3

Colorectal cancer (CRC) is one of the most common solid tumors worldwide and has an extremely poor prognosis. MicroRNA-429 (miR-429) has been reported to participate in the progression of CRC. However, the pathological mechanisms require further investigation. The aim of the present study was to investigate the association between miR-429 and high mobility group box 3 (HMGB3) in CRC and the associated mechanism. The mRNA expression levels of miR-429 and HMGB3 in 65 paired CRC and adjacent tissues were examined by reverse transcription-quantitative PCR. Furthermore, a dual-luciferase reporter assay was performed to identify the association between miR-429 and HMGB3. Finally, the effects of miR-429 and HMGB3 on the proliferation and apoptosis of CRC cells were detected. As a result, it was identified that miR-429 expression was downregulated and HMGB3 expression was upregulated in CRC tissues compared with in adjacent non-cancer tissues, and the expression levels of miR-429 were negatively associated with those of HMGB3. Notably, HMGB3 was demonstrated to be a direct target of miR-429 by dual-luciferase reporter assay. Furthermore, transfection with a miR-429 mimic significantly inhibited HMGB3 expression and led to decreased proliferation and increased apoptosis of CRC cells. On the other hand, transient overexpression of HMGB3 partially inhibited the antitumor effects of miR-429. To the best of our knowledge, the present study demonstrated for the first time that miR-429 regulated the proliferation and apoptosis of CRC cells via HMGB3, suggesting a specific tumor suppressive function of the miR-429/HMGB3 signaling pathway in CRC.
Challenges and Opportunities for Drug Repositioning in Fibrodysplasia Ossificans Progressiva

Fibrodysplasia ossificans progressiva (FOP) is an ultrarare congenital disease that progresses through intermittent episodes of bone formation at ectopic sites. FOP patients carry heterozygous gene point mutations in activin A receptor type I ACVR1, encoding the bone morphogenetic protein (BMP) type I serine/threonine kinase receptor ALK2, termed activin receptor-like kinase (ALK)2. The mutant ALK2 displays neofunctional responses to activin, a closely related BMP cytokine that normally inhibits regular bone formation. Moreover, the mutant ALK2 becomes hypersensitive to BMPs. Both these activities contribute to enhanced ALK2 signalling and endochondral bone formation in connective tissue. Being a receptor with an extracellular ligand-binding domain and intrinsic intracellular kinase activity, the mutant ALK2 is a druggable target. Although there is no approved cure for FOP yet, a number of clinical trials have been recently initiated, aiming to identify a safe and effective treatment for FOP. Among other targeted approaches, several repurposed drugs have shown promising results. In this review, we describe the molecular mechanisms underlying ALK2 mutation-induced aberrant signalling and ectopic bone formation. In addition, we recapitulate existing in vitro models to screen for novel compounds with a potential application in FOP. We summarize existing therapeutic alternatives and focus on repositioned drugs in FOP, at preclinical and clinical stages.
A Neurophysiological Pattern as a Precursor of Work-Related Musculoskeletal Disorders Using EEG Combined with EMG

We aimed to determine the neurophysiological pattern that is associated with the development of musculoskeletal pain that is induced by biomechanical constraints. Twelve (12) young healthy volunteers (two females) performed two experimental realistic manual tasks for 30 min each: (1) with the high risk of musculoskeletal pain development and (2) with low risk for pain development. During the tasks, synchronized electroencephalographic (EEG) and electromyography (EMG) signals data were collected, as well as pain scores. Subsequently, two main variables were computed from neurophysiological signals: (1) cortical inhibition as Task-Related Power Increase (TRPI) in beta EEG frequency band (β.TRPI) and (2) muscle variability as Coefficient of Variation (CoV) from EMG signals. A strong effect size was observed for pain measurement under the high risk condition during the last 5 min of the task execution; with muscle fatigue, because the CoV has decreased below 18%. An increase in cortical inhibition (β.TRPI >50%) was observed after the 5th min of the task in both experimental conditions. These results suggest the following neurophysiological pattern—β. TRPI ≥ 50% and CoV ≤ 18%—as a possible indicator to monitor the development of musculoskeletal pain in the shoulder in the context of repeated and prolonged exposure to manual tasks.
Chloroquine and Hydroxychloroquine: Efficacy in the Treatment of the COVID-19

Chloroquine (CQ) and its derivative, hydroxychloroquine (HCQ), have attracted wide attention for treating coronavirus disease 2019 (COVID-19). However, conflicting outcomes have been found in COVID-19 clinical trials after treatment with CQ or HCQ. To date, it remains uncertain whether CQ and HCQ are beneficial antiviral drugs for combating COVID-19. We performed a systematic review to depict the efficacy of CQ or HCQ for the treatment of COVID-19. The guidelines of PRISMA were used to conduct this systematic review. We searched through articles from PubMed, Web of Science and other sources that were published from 1 January 2020 to 31 October 2020. The search terms included combinations of human COVID-19, CQ, and HCQ. Eleven qualitative articles comprising of four clinical trials and seven observation studies were utilized in our systematic review. The analysis shows that CQ and HCQ do not have efficacy in treatment of patients with severe COVID-19. In addition, CQ and HCQ have caused life-threatening adverse reactions which included cardiac arrest, electrocardiogram modification, and QTc prolongation, particularly during the treatment of patients with severe COVID-19. Our systematic review suggested that CQ and HCQ are not beneficial antiviral drugs for curing patients with severe COVID-19. The treatment effect of CQ and HCQ is not only null but also causes serious side effects, which may cause potential cardiotoxicity in severe COVID-19 patients.
Ocoxin Increases the Antitumor Effect of BRAF Inhibition and Reduces Cancer Associated Fibroblast-Mediated Chemoresistance and Protumoral Activity in Metastatic Melanoma

Whereas the prevalence of several cancer types is decreasing, skin malignancies are growing more common every year. Malignant melanoma is the most aggressive form of skin cancer with high metastatic capacity. In most cases, malignant melanoma shows acquired therapy resistance. We evaluated the ability of Ocoxin, a natural compound-based antioxidant and anti-inflammatory nutritional complement, to exert an antitumor effect in melanoma. To do so, the cytotoxicity of Ocoxin in a panel of BRAF-mutated murine and human melanoma cell lines was tested alone and in combination with BRAF inhibitor Vemurafenib. Our results revealed a potent cytotoxic effect of Ocoxin against melanoma cells and a synergic effect when combined with Vemurafenib, reducing viability and increasing apoptosis. Besides, Ocoxin interferes with the cell cycle, impairs the inherent and fibroblast-mediated melanoma cell migration, and reduces resistance to BRAF inhibition. Proteomic analysis revealed reduced tumor secretion of inflammatory factors Galectin-1, Osteopontin, CCL5, and CCL9 upon treatment with Ocoxin. Moreover, RNASeq showed that Ocoxin downregulated the cell cycle and proliferation-related genes. In vivo, Ocoxin reduced the number of lung metastasis of YUMM-1.7 melanoma cells. Therefore, Ocoxin arises as a good candidate for clinical trials analyzing the beneficial effects in patients suffering from this cutaneous malignancy.