Interactions between HIV protease inhibitor ritonavir and human DNA repair enzyme ALKBH2: a molecular dynamics simulation study.

The human DNA repair enzyme AlkB homologue-2 (ALKBH2) repairs methyl adducts from genomic DNA. Overexpression of ALKBH2 has been implicated in both tumorigenesis and chemotherapy resistance in some cancers, including glioblastoma and renal cancer rendering it a potential therapeutic target and a diagnostic marker. However, no inhibitor is available against these important DNA repair proteins. Intending to repurpose a drug as an inhibitor of ALKBH2, we performed in silico evaluation of HIV protease inhibitors and identified Ritonavir as an ALKBH2-interacting molecule. Using molecular dynamics simulation, we elucidated the molecular details of Ritonavir-ALKBH2 interaction. The present work highlights that Ritonavir might be used to target the ALKBH2-mediated DNA alkylation repair.

Human RAD51 paralogue RAD51C fosters repair of alkylated DNA by interacting with the ALKBH3 demethylase.

The integrity of our DNA is challenged daily by a variety of chemicals that cause DNA base alkylation. DNA alkylation repair is an essential cellular defence mechanism to prevent the cytotoxicity or mutagenesis from DNA alkylating chemicals. Human oxidative demethylase ALKBH3 is a central component of alkylation repair, especially from single-stranded DNA. However, the molecular mechanism of ALKBH3-mediated damage recognition and repair is less understood. We report that ALKBH3 has a direct protein-protein interaction with human RAD51 paralogue RAD51C. We also provide evidence that RAD51C-ALKBH3 interaction stimulates ALKBH3-mediated repair of methyl-adduct located within 3'-tailed DNA, which serves as a substrate for the RAD51 recombinase. We further show that the lack of RAD51C-ALKBH3 interaction affects ALKBH3 function in vitro and in vivo. Our data provide a molecular mechanism underlying upstream events of alkyl adduct recognition and repair by ALKBH3.

Heteroexpression of Mycobacterium leprae hypothetical protein ML0190 provides protection against DNA-alkylating agent methyl methanesulfonate.

Repair of DNA alkylation damage is essential for maintaining genome integrity and Fe(II)/2-oxoglutarate(2OG)-dependent dioxygenase family of enzymes play crucial role in repairing some of the alkylation damages. Alkylation repair protein-B (AlkB) of Escherichia coli belongs to Fe(II)/2OG-dependent dioxygenase family and carries out DNA dealkylation repair. We report here identification of a hypothetical Mycobacterium leprae protein (accession no. ML0190) from the genomic database and show that this 615-bp open reading frame encodes a protein with sequence and structural similarity to Fe(II)/2OG-dependent dioxygenase AlkB. We identified mRNA transcript of this gene in the M. leprae infected clinical skin biopsy samples isolated from the leprosy patients. Heterologous expression of ML0190 in methyl methane sulfonate (MMS) sensitive and DNA repair deficient strain of Saccharomyces cerevisiae and Escherichia coli resulted in resistance to alkylating agent MM. The results of the present study imply that Mycobacterium leprae ML0190 is involved in protecting the bacterial genome from DNA alkylation damage.

Escherichia coli AlkB interacts with single-stranded DNA binding protein SSB by an intrinsically disordered region of SSB.

Intrinsically disordered regions (IDRs) of proteins often regulate function through interactions with folded domains. Escherichia coli single-stranded DNA binding protein SSB binds and stabilizes single-stranded DNA (ssDNA). The N-terminal of SSB contains characteristic OB (oligonucleotide/oligosaccharide-binding) fold which binds ssDNA tightly but non-specifically. SSB also forms complexes with a large number proteins via the C-terminal interaction domain consisting mostly of acidic amino acid residues. The amino acid residues located between the OB-fold and C-terminal acidic domain are known to constitute an IDR and no functional significance has been attributed to this region. Although SSB is known to bind many DNA repair protein, it is not known whether it binds to DNA dealkylation repair protein AlkB. Here, we characterize AlkB SSB interaction and demonstrate that SSB binds to AlkB via the IDR. We have established that AlkB-SSB interaction by in vitro pull-down and yeast two-hybrid analysis. We mapped the site of contact to be the residues 152-169 of SSB. Unlike most of the SSB-binding proteins which utilize C-terminal acidic domain for interaction, IDR of SSB is necessary and sufficient for AlkB interaction.

Immunoinformatics-driven approach for development of potential multi-epitope vaccine against the secreted protein FlaC of Campylobacter jejuni.

Campylobacter jejuni causes a leading human gastrointestinal infection which is associated with foodborne diarrhea, stomach cramping, and fever. In the recent years, numerous multidrug-resistant strains of C. jejuni has evolved and is considered in the priority pathogens category. Therefore, an increasing demand exists to develop an effective vaccine against Campylobacteriosis. The T cell and B cell epitopes from the FlaC protein were predicted using comprehensive immunoinformatics tools. The predicted epitopes were chosen based on their antigenicity, allergenicity, and toxicity profiles. Using the bioinformatics approach various physicochemical properties of the constructed vaccine were determined. The molecular docking analysis of the vaccine with the TLRs demonstrated that TLR5 has a higher binding affinity of -1159.0 kcal/mol. Molecular dynamics simulation has confirmed the stable association of the vaccine with TLR5. The immune response of the constructed vaccine was validated using immunostimulation. Based on this study, we recommend the formulation of a multi-epitope vaccine as a promising agent to effectively combat the dreadful campylobacteriosis infection.Communicated by Ramaswamy H. Sarma.

GC-MS analysis, pharmacokinetic properties, molecular docking and dynamics simulation of bioactives from Curcumis maderaspatanus to target oral cancer.

Oral cancer (OC) which is the most predominant malignant epithelial neoplasm in the oral cavity, is the 8th commonest type of cancer globally. Natural products are excellent sources of functionally active compounds and essential nutrients that play an important role in cancer therapeutics. Using the structure-based virtual screening, drug-likeness, toxicity, and molecular dynamics simulation, the current study focused on the evaluation of anticancer activity of bioactive compounds from Curcumis maderaspatanus. AURKA, CDK1, and VEGFR-2 proteins which play a crucial role in the development and progression of oral cancer was selected as targets and 216 phytochemicals along with a known reference inhibitor were docked against these target proteins. Based on the docking score, it was found that phytochemicals namely 3-Benzoyl-2,4(1H,3H)-Pyrimidinedione (- 8.0 kcal/mol), 1-Cyclohexylethanol, trifluoroacetate (- 6.3 kcal/mol), and Alpha-Curcumene (- 8.9 kcal/mol) interacts with AURKA, CDK1, and VEGFR-2 with highest binding affinity. The molecular dynamics simulation demonstrated that the best docked complexes exhibited excellent structural stability in terms of RMSD, RSMF, SASA and Rg for a period of 100 ns. Altogether, our computational analysis reveals that the bioactives from C. maderaspatanus could emerge as efficacious drug candidates in oral cancer therapy. Supplementary Information: The online version contains supplementary material available at 10.1007/s40203-023-00177-x.

Participatory research in mental health care services in low- and middle-income countries: a scoping review protocol.

OBJECTIVE: The objective of this scoping review will be to identify and map the characteristics of participatory research approaches in mental health care services conducted in low- and middle-income countries (LMICs). INTRODUCTION: Developing countries have a treatment gap of 76% to 85% for mental disorders. Participatory research can help understand community perspectives, which, in turn, helps develop sustainable, contextually specific services. Although participatory research appears promising, especially in the context of LMICs, the field is heterogenous in terms of the methods used; the various stakeholders; the design, implementation, and evaluation of services; and outcome measures. INCLUSION CRITERIA: This review will include all studies on participatory research in mental health care services in LMICs. All types of participants (ie, children/adolescent/adults, gender, rural/urban, etc.) and settings will be considered. METHODS: The proposed review will follow the JBI methodology for scoping reviews. Published and unpublished studies will be searched for in MEDLINE (PubMed), Embase (Ovid), PsycINFO (EBSCOhost), CINAHL (EBSCOhost), and Google Scholar (first 10 pages). We will also search for gray literature and screen reference lists of relevant reviews. Two independent reviewers will screen the titles and abstracts of the studies, followed by full-text screening. Data will be extracted using a predefined form. The findings will be descriptively presented with supporting tables and diagrams, accompanied by a narrative summary. REVIEW REGISTRATION: Details of the review can be found in Open Science Framework https://osf.io/cn54r.

Surgical management of oculomotor nerve palsy: a comparison of lateral rectus deactivation combined with either medial rectus resection or medial rectus fixation to the medial palpebral ligament.

PURPOSE: To analyze and compare the outcome of two different surgical procedures in patients with complete oculomotor nerve palsy with large-angle exotropia. METHODS: The medical records of patients with total oculomotor nerve palsy and large-angle exotropia operated on at a single center from January 2006 to June 2020 were reviewed retrospectively. One group underwent lateral rectus deactivation with medial rectus resection (resection group); the other group underwent lateral rectus deactivation with medial rectus fixation to the medial palpebral ligament (fixation group). Surgical outcomes on the first postoperative day and at 6 months postoperatively were analyzed, including alignment and postoperative complications. All statistical analyses were performed using STATA version 14. A P value of <0.05 was considered significant. RESULTS: A total of 35 patients were included. There was a trend toward greater surgical success in the fixation group (93%) than in the resection group (65%), but these results were not statistically significant. Postoperative exotropic drifts were noted in both the procedures but tended to be more with patients in the resection group. Postoperative complications were noted only in the fixation group. CONCLUSIONS: Lateral rectus deactivation with medial rectus fixation to the medial palpebral ligament requires more time and greater surgical expertise but appears to better prevent postoperative exotropic drift compared with lateral rectus deactivation combined with medial rectus resection.

Effect of webinars in teaching-learning process in medical and allied health science students during COVID-19 pandemic: A cross-sectional study.

BACKGROUND: COVID-19 pandemic lockdown has brought all sectors to be dwindled with no exception of the academic system. Even professional courses like medical and allied health academic courses were also not spared. The academic requirements were not met as required to do so. Webinar has become a good source of virtual platform acting as a bridge for attaining the gaps in accomplishing the curriculum to the students during these curfew times. Our study aimed to know the value of webinars on teaching-learning processes among the medical and allied health science students in India. MATERIALS AND METHODS: The study design is a cross-sectional study with 2084 students who attended at least one webinar. An online survey questionnaire was sent, and the data were collected on participant's perspective on the effectiveness of webinar, post webinar assessment by their satisfactory level of gain of information through webinars and their plan to apply in future. RESULTS: Participant's perspective on effectiveness of webinar showed 66.7% of agreement with the webinar use. In post webinar assessment, the use of webinar was in agreement with 69.9% of the participants. Furthermore, we observed a significant association with the gain of information in post webinar assessment (P < 0.05) and a significant association with their plan to apply in future (P < 0.05). CONCLUSION: Our results showed that the students were satisfied with the webinar teaching and acknowledged it to be an effective tool in the teaching-learning process to gain new knowledge and wish to attend webinars in future as a part of their curriculum. Thus, webinars have a constructive effect in the teaching and learning process in professional courses during pandemic lockdown.

Nanotechnology-assisted production of value-added biopotent energy-yielding products from lignocellulosic biomass refinery - A review.

The need to develop sustainable alternatives for pretreatment and hydrolysis of lignocellulosic biomass (LCB) is a massive concern in the industrial sector today. Breaking down of LCB yields sugars and fuel in the bulk scale. If explored under nanotechnology, LCB can be refined to yield high-performance fuel sources. The toxicity and cost of conventional methods can be reduced by applying nanoparticles (NPs) in refining LCB. Immobilization of enzymes onto NPs or used in conjugation with nanomaterials would instill specific and eco-friendly options for hydrolyzing LCB. Nanomaterials increase the proficiency, reusability, and stability of enzymes. Notably, magnetic NPs have bagged their place in the downstream processing of LCB effluents due to their efficient separation and cost-effectiveness. The current review highlights the role of nanotechnology and its particles in refining LCB into various commercial precursors and value-added products. The relationship between nanotechnology and LCB refinery is portrayed effectively in the present study.

Symmetrical and un-symmetrical curcumin analogues as selective COX-1 and COX-2 inhibitor.

Curcumin, a popular herbal medicine derived from turmeric, blocks the synthesis of prostaglandins by inhibiting Cyclooxygenase-1 and 2 (COX-1 and COX2). We have recently reported an efficient method of synthesizing curcumin and synthesised analogues. In the present study, we have investigated sixteen novel analogues of curcumin for their ability to inhibit COX-1 and COX-2. We report here that most of the curcumin analogues display selective inhibition of COX-2, whereas a few suppress COX-1 activity. Further, we examined the binding of these inhibitors by molecular docking and observed that the compound with pronounced selectivity for COX-2 displayed better binding to COX-2 compared to curcumin.

Escherichia coli AlkB and single-stranded DNA binding protein SSB interaction explored by Molecular Dynamics Simulation.

Repair of alkylation damage in DNA is essential for maintaining genome integrity. Escherichia Coli (E.coli) DNA repair enzyme AlkB removes methyl adducts including 1-methyladenine and 3-methylcytosine present in DNA by oxidative demethylation from single-stranded DNA (ssDNA). E. coli single-stranded DNA binding protein (SSB) selectively binds ssDNA in a sequence-independent manner. We have recently shown that AlkB can repair methyl adduct present in SSB-coated ssDNA. In this study, we aimed to elucidate details of AlkB-mediated DNA repair of SSB-bound DNA substrate. Therefore, we generated a structural model of AlkB-SSB-ssDNA and using Molecular Dynamics simulation analysis we show that flexibility of SSB-bound DNA allows AlkB to bind in multiple ways. Our docking analysis of AlkB-SSB-ssDNA structure revealed that the Cyt109 base is present in the hydrophobic cavity of AlkB active site pocket. The characterization of AlkB-SSB interaction pattern would likely to help in understanding the mode of alkylated DNA adduct recognition by AlkB.

New biomarkers in brain trauma.

Brain-specific biomolecules are being increasingly investigated as a viable alternative to the clinical scores and radiological features, on which we still rely upon for stratification, therapy and predicting outcome in traumatic brain injury (TBI). TBI generally leads to release of various chemical compound within the cerebrospinal fluid (CSF) or blood depending on the severity of injury, which were studied variedly in last decades. However, most of these compounds being non-specific to brain, their applicability was challenged further. This review encompasses the novel and promising biomarkers being studied in the present decade, with encouraging results in laboratory and animal or human models.