Targeting BRF2: insights from in silico screening and molecular dynamic simulations.

The Transcription factor II B (TFIIB)­related factor 2 (BRF2) containing TFIIIB complex recruits RNA polymerase III multi-subunit complex to selective gene promoters that altogether are responsible for synthesizing a variety of small non-coding RNAs, including a special type of selenocysteine tRNA (tRNASec), micro-RNA (miRNA), and other regulatory RNAs. BRF2 has been identified as a potential oncogene that promotes cancer cell survival under oxidative stress through its genetic activation. The structure of the BRF2 protein was modeled using the Robetta server, refined, and validated using the Ramachandran plot. A virtual approach utilizing molecular docking was used to screen a natural compound library to determine potential compounds that can interact with the molecular pin motif of the BRF2 protein using Maestro (Schrodinger). Subsequent molecular dynamics simulation studies of the top four ligands that exhibited low glide scores were performed using GROMACS. The findings derived from the simulations, in conjunction with the exploration of hydrogen bonding patterns, evaluation of the free energy landscape, and thorough analysis of residue decomposition, collectively converged to emphasize the robust interaction characteristics exhibited by Ligand 366 (Deacetyl lanatoside C) and ligand 336 (Neogitogenin)-with the BRF2 protein. These natural compounds may be potential inhibitors of BRF2, which could modulate the regulation of selenoprotein synthesis in cancer cells. Targeting BRF2 using these promising compounds may offer a new therapeutic approach to sensitize cancer cells to ferroptosis and apoptosis.Communicated by Ramaswamy H. Sarma.

Identification of coastal pesticide pollutants as potent inhibitors of Bacillus pasteurii urease mediated calcium carbonate precipitation: a computational approach.

Microbially induced calcite precipitation (MICP) through urease enzyme has attained a lot of recognition in various fields of civil engineering and geotechnology for stabilizing the strength of soil and various concrete materials. The activity of urease has been found to be affected by various factors like temperature, substrate concentrations, pH of the medium, presence of inhibitors, etc. Through this study, the outcome of the interaction of pesticides (commonly found in Indian coastal regions) on Bacillus pasteurii urease, a major organism reported for MICP studies has been investigated in silico. The results from the study revealed that the enzyme has higher interactions of -4.1, -3.2, and -3.4 kJ/mol with common pesticides like dichloro diphenyl dichloro ethane(DDD), dichloro diphenyl trichloroe thane (DDT), and methyl parathion of organochlorides and organophosphates class. From the molecular dynamics simulation analysis, complex 1 (DDD -receptor) has been found to have the highest and more compact structure followed by methyl parathion -receptor. Prime MM-GBSA analysis also revealed the highest binding energy of -27.8 kcal/mol with the protein and DDD. Thus, it can be inferred from the current study that pesticides, particularly, DDD, DDT, and methyl parathion present in the coastal areas may have an impact on urease. This interaction can result in the inhibition of the urease activity of B. pasteurii, thus preventing the biomineralization process. This study would be the first report on the computational approach to understanding the interaction of prominent pesticides on the coastal region and B. pasteurii urease.Communicated by Ramaswamy H. Sarma.

Identification of CXCR4 inhibitors as a key therapeutic small molecule in renal fibrosis.

The final stage of almost all chronic kidney diseases is renal fibrosis. Simple wounds or persistent inflammation can cause tissue inflammation, which, in the case of the kidney, results in scarring. Vascular sclerosis, tubulointerstitial fibrosis and glomerular fibrosis are all types of kidney fibrosis. Renal damage and fibrosis are caused by elevated expression of CXCR4. This study aimed to identify possible pharmacological agents which could bind to and inhibit isoform I of CXCR4 and determine their strength of interactions. The I-TASSER, Galaxyweb and Robetta were used to predict and refine the structure of the CXCR4 protein. ModBase was used to improve the loops, and then the quality was evaluated by using the ERRAT value (92.15) and Ramachandran plot. The improved 3D structure was subjected to small molecule database docking using Maestro (from Schrodinger) and the glide module. GROMACS was used to simulate molecules with the three top low glide scores and the best ADME properties. The best glide score was achieved by ligand ID 4990 (-11.5). Simulations, free energy landscape and residue decomposition analysis revealed that 4990 interacted more consistently with CXCR4 than the other two small molecules.Communicated by Ramaswamy H. Sarma.

In silico identification of a promising inhibitor of Fusarium oxysporum f. sp. Lycopersici, Secreted in Xylem 1 protein.

Fusarium oxysporum f. sp. Lycopersici (FOL) is a soilborne pathogen that infects tomato plants and inflicts severe damage, resulting in heavy yield losses worldwide, causing Fusarium wilt disease. FOL encodes several pathogenicity factors necessary for colonizing and invading the host plants. Secreted in Xylem (SIX), a pathogenicity factor, is a small cysteine-rich fungal protein found in the xylem sap of FOL-infected tomato plants, which plays a major role in determining host specificity and in contributing to pathogenicity/virulence. However, the structure of SIX1 has not been modeled yet. Therefore, this study aimed to elucidate the structure of SIX1 by comparative modeling using Robetta server. The best possible structures obtained were then refined, validated, and utilized for subsequent analysis. An antifungal library comprising 16,824 compounds was screened to determine small molecules that can interact with SIX1. Five antifungal compounds were identified from the library. Further analyses revealed that, of the five ligands, 4-[(2-(3-methoxyphenoxy)acetyl)amino] benzamide exhibited the capacity to stably interact with SIX1. This shows that 4-[[2-(3-methoxyphenoxy)acetyl]amino] benzamide can be used as a potential candidate in the prevention of FOL infection. In summary, small-molecule inhibitors such as 4-[[2-(3-methoxyphenoxy)acetyl]amino] benzamide could be highly effective in combating FOL infection, along with biocontrol methods and strategies that use transgenic plants overexpressing resistance genes.

Development of a smart pH-responsive nano-polymer drug, 2-methoxy-4-vinylphenol conjugate against the intestinal pathogen, Vibrio cholerae.

Vibrio cholerae causes cholera, an acute diarrhoeal disease. The virulence in V. cholerae is regulated by the quorum-sensing mechanism and response regulator LuxO positively regulates the expression of virulence determinants adhesion, biofilm formation, and cholera toxin production. Previous in-silico studies revealed that 2-methoxy-4-vinylphenol could bind to the ATP binding site of LuxO and the complex was compact and stable in pHs like intestinal pHs. Here, we have explored the polymeric nano-formulation of 2-methoxy-4-vinylphenol using cellulose acetate phthalate for controlled drug release and their effectiveness in attenuating the expression of V. cholerae virulence. Physico-chemical characterization of the formulation showed particles with a mean size of 91.8 ± 14 nm diameter and surface charge of - 14.7 ± 0.07 mV. The uniform round polymeric nanoparticles formed displayed about 51% burst release of the drug at pH 7 by 3rd h, followed by a controlled linear release in alkaline pH. The polymeric nanoparticles demonstrated a tenfold increase in intestinal membrane permeability ex-vivo. At lower concentrations, the 2-methoxy-4-vinylphenol polymeric nanoparticles were non-cytotoxic to Int 407 cells. In-vitro analysis at pH 6, pH 7, pH 8, and pH 9 revealed that cellulose acetate phthalate-2-methoxy-4-vinylphenol nanoparticles were non-bactericidal at concentrations up to 500 µg/mL. At 31.25 µg/mL, the nanoparticles inhibited about 50% of the biofilm formation of V. cholerae MTCC 3905 and HYR14 strains. At this concentration, the adherence of V. cholerae MTCC 3905 and HYR14 to Int 407 cell lines were also significantly affected. Gene expression analysis revealed that the expression of tcp, qrr, and ct at pH 6, 7, 8, and 9 has reduced. The CAP-2M4VP nanoparticles have demonstrated the potential to effectively reduce the virulence of V. cholerae in-vitro.

Refractive Error among Children Visiting the Department of Paediatric Opthalmology of a Tertiary Eye Care Center.

Introduction: Refractive error is the inability of eyes to focus clearly on images. Visual impairment due to refractive error has a major impact on children's education and daily activities. The hospital has no documentation of the ocular morbidity related to refractive errors in children. The aim of this study was to find out the prevalence of refractive error in children visiting the Department of Paediatric Ophthalmology of a tertiary care centre. Methods: A descriptive cross-sectional study was done in the Outpatient Department of Paediatric Ophthalmology in a tertiary care centre from 8 September 2022 to 7 March 2023 after obtaining ethical approval from the Institutional Review Committee. A convenience sampling method was used. The point estimate was calculated at 95% Confidence Interval. Results: Among 3600 children, the prevalence of refractive error was seen in 668 children (18.56%) (15.61-21.51, 95% Confidence Interval). Refractive error was seen in 363 (54.34%) boys and 305 (45.66%) girls. Myopia was found in 340 (50.90%), astigmatism in 207 (30.99%), and hyperopia in 121 (18.11%). Conclusions: The prevalence of refractive error among children attending a tertiary care centre was found to be higher than studies done in similar settings. Regular screening of refractive error for visual impairment is recommended among school going children. Keywords: astigmatism; hyperopia; myopia; refractive error; visual impairment.

Prevalence of Retinitis Pigmentosa in a Tertiary Eye Hospital of Nepal.

INTRODUCTION: Retinitis Pigmentosa (RP) is a group of diffuse retinal degenerative diseases predominantly affecting the rod and cone photoreceptors. The prevalence of retinitis pigmentosa seen in literature is approximately 1:4000. Retinitis Pigmentosa is one of the the most common causes of blindness in the age group of 20 to 40 years. The objective of this study was to determine the profile of retinitis pigmentosa in Terai and Nepal-India border region considering patients seeking care at a Tertiary level Eye Hospital in the terai region (southern part) of Nepal. MATERIALS AND METHODS: A hospital-based, retrospective study was carried out at R. M. Kedia Eye Hospital. A total of 385 (83 males and 107 females from Nepal and 109 males and 86 females from India) diagnosed patients of Retinitis Pigmentosa were included in the study. Data was collected over a period of eleven years from 2008-2018. RESULTS: Out of 385 diagnosed Retinitis Pigmentosa patients, 192 (49.87%) were male and 193 (50.13%) were female with slightly female predominance. The prevalence of RP seen in our study was 0.03%. About 51% of the patients visited here were from India and nearby border areas/ villages which cover most of the rural areas of India. In this study it was found that 49.34% of the RP cases were from Nepal, of which 43.63% of cases were from Hindu community and 5.71% from Muslim community and about 50.66% cases of RP were from India, of which 37.67% from Hindu and 12.98% from Muslim community. The peak age of presentation of RP was at 30-39 years (29.09%), followed by 20-29 years (26.75%). The common marriage pattern of consanguinity was found in Muslim community in between the first cousins. In this study the hospital record did not show any evaluation for the syndromic disease in the hospital record, though RP is usually non syndromic and there are literatures where many syndromic forms have been identified. CONCLUSION: The prevalence of RP seen in the study was 0.03% (A total of 1101299 sample population of which 385 patients had RP). Since RP is an inherited disease and is one of the non-treatable causes of blindness which runs in the families, a role of counseling to reduce consanguineous marriages should be brought forward to reduce the disease process.

A Review on Pharmacokinetics Properties of Antiretroviral Drugs to Treat HIV-1 Infections.

BACKGROUND: The HIV-1 pandemic is undoubtedly the major public-health crisis of our time. The extensive research on HIV has deepened our understanding of its pathogenesis and transmission dynamics. Some new entity molecules have been approved by the FDA for HIV treatment, but till now, the protective vaccine remains elusive. Scientists are targeting many important proteins of HIV-1; gp41, gp120, CCR5 coreceptor, integrase, reverse transcriptase and protease. Few compounds are used as nucleotide analogues to stop HIV replication. Altogether, these compounds and their derivatives specifically block HIV entry and DNA replication. Using ADMET studies, people are working on these compounds to reduce toxicity and increase potency. OBJECTIVES: Our main aim is to discuss the Pharmacokinetics properties of 23 important FDA antiretroviral drugs used for the treatment of HIV-1 infections. METHODS: We have searched literature related to pharmacokinetics properties in PubMed, Google Scholar search engine. CONCLUSION: Here, we have reviewed the pharmacokinetic properties such as absorption, bioavailability, distribution, metabolism, and excretion of 23 important FDA-approved drugs. These drugs are Fuzeon, Selzentry, Complera, Epivir, Retrovir, Emtriva, Ziagen, Edurant, Intelence, Pifeltro, Sustiva, Viramune, Isentress, Genvoya, Tivicay, Reyataz, Prezista, Lexiva, Invirase, Aptivus etc. classified into five major classes: fusion inhibitors, Nucleoside/Nucleotide Reverse Transcriptase Inhibitors (NRTIs), Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs), Integrase Strand transfer inhibitors (INSTIs) and Protease inhibitors (PIs). This review may be helpful for the future development of potent antiretroviral drugs with improved pharmacokinetic properties.

Constitutive Inflammatory Cytokine Storm: A Major Threat to Human Health.

Immune cells secrete small protein molecules that aim for cell-cell communications. These small molecules are called cytokines. Targeting cancer cells with administration of bispecific antibodies and natural extracts results in elevated circulating levels of inflammatory cytokines, including interferon-γ and interleukin (IL)-6, which lead to cell toxicity. Sustained release of cytokines due to immunotherapy or hormonal issues causes various diseases. Novel T cell-engaging therapies and monoclonal antibodies cause cytokine release syndrome. Efforts are being carried out to maximize the chance for therapeutic benefit from immunotherapy while minimizing the risk for life-threatening complications of sustained cytokine release. Neurodegeneration and cardiac diseases are the prominent diseases caused by inflammatory cytokines. The phenomenon is called cytokine storm. Cytokines can act antagonistically or synergistically. Constitutive expression of proinflammatory cytokines such as IL-3 and IL-6 causes organ damage and unbearable pain. In this review, we will discuss the regulators of cytokine release, its types, its implications on human health, and treatment.

Cdk5: A main culprit in neurodegeneration.

Objectives: Neurodegenerative diseases (NDs) such as Alzheimer Diseases (AD), Parkinson Diseases (PD) are a huge public health problem. The elucidation of their pathophysiological mechanism is one of our greatest challenges. Hyperactive immune system contributes to the pathophysiology of neurological disorders. Methods: In this review article, we have highlighted the neurodegenerative role of CDK5 and its involvement in Amyloid precursor pathway via Beta secretase enzyme. Results:All the landmark research reports for CDK5 were considered for this review and its involvement in disrupted autophagy and hyper immune response is the key cause for neurodegeneration. Conclusion: In conclusion, the present review focus on the pathways associated with Cdk5 and its role in causing neurodegeneration.

Scale-up and inhibitory studies on productivity of lipase from Acinetobacter radioresistens PR8.

Acinetobacter radioresistens PR8 produces extracellular lipase depending upon growth media. In present work we not only screened the nutrient sources but also investigated the causes for variation in productivity. The nutrient sources investigated are, groundnut oil, groundnut cake and fresh groundnut. Lower lipase productivity was observed on fresh ground nut in contrast to groundnut oil and groundnut cake. The lipase productivity was examined in the batch and parameters monitored were bacterial growth, enzyme activity, pH, lipids and protein concentration. The aflatoxin B1 and oxalic acid present in fresh groundnut were found to be responsible for lower lipase productivity. The interaction studies of oxalic acid and purified lipase was confirmed with CD spectra analysis, isothermal titration calorimetry studies and fluorescence quenching. Therefore, the importance of economical cheap groundnut cake with no aflatoxin B1 and oxalates are proposed to be used for optimum lipase production.

Molecular docking and simulation studies of gustatory receptor of Aedes aegypti: A potent drug target to distract host-seeking behaviour in mosquitoes.

BACKGROUND & OBJECTIVES: It is well reported that exhaled CO 2 and skin odour from human being assist female mosquitoes to locate human host. Basically, the receptors for this activity are expressed in cpA neurons. In both Aedes aegypti and Anopheles gambiae, this CO 2-sensitive olfactory neuron detects myriad number of chemicals present in human skin. Therefore, manipulation of gustatory receptors housing these neurons may serve as important targets for behavioural intervention. The study was aimed towards virtual screening of small molecules in the analyzed conserved active site residues of gustatory receptor and molecular dynamics simulation study of optimum protein-ligand complex to identify a suitable lead molecule for distracting host-seeking behaviour of mosquitoes. METHODS: The conserved residue analysis of gustatory receptor (GR) of Ae. aegypti and An. gambiae was performed. The structure of GR protein from Ae. aegypti was modeled and validated, and then molecular docking was performed to screen 2903 small molecules against the predicted active residues of GR. Further, simulation studies were also carried out to prove protein-ligand stability. RESULTS: The glutamine 154 residue of GR was found to be highly conserved in Ae. aegypti and An. gambiae. Docking results indicated that the dodecanoic acid, 1,2,3-propanetriyl ester (dynasan 112) was interacting with this residue, as it showed better LibDock score than previously reported ethyl acetate used as mosquito repellant. Simulation studies indicated the structural instability of GR protein in docked form with dynasan 112 suggesting its involvement in structural changes. Based on the interaction energies and stability, this compound has been proposed to be used in mosquitoes' repellant. INTERPRETATION & CONCLUSION: A novel effective odorant acting as inhibitor of GR is proposed based on its stability, docking score, interactions and RMSD, considering ethyl pyruvate as a standard inhibitor. Host preference and host-seeking ability of mosquito vectors play key roles in disease transmission, a clear understanding of these aspects is essential for preventing the spread of the disease.

Alzheimer disease: An interactome of many diseases.

Alzheimer Disease (AD) is an outcome as well as source of many diseases. Alzheimer is linked with many other diseases like Diabetes type 2, cholesterolemia, hypertension and many more. But how each of these diseases affecting other is still unknown to scientific community. Signaling Pathways of one disease is interlinked with other disease. But to what extent healthy brain is affected when any signaling in human body is disturbed is the question that matters. There is a need of Pathway analysis, Protein-Protein interaction (PPI) and the conserved interactome study in AD and linked diseases. It will be helpful in finding the potent drug or vaccine target in conscious manner. In the present research the Protein-Protein interaction of all the proteins involved in Alzheimer Disease is analyzed using ViSANT and osprey tools and pathway analysis further reveals the significant genes/proteins linking AD with other diseases.