Target-based virtual screening and molecular dynamics approach to identify potential antileishmanial agents through targeting UvrD-like helicase ATP-binding domain

Background: About 0.7-1.0 million people worldwide have been suffering from Leishmaniasis. It falls under a neglected tropical disease (NTD) and is transmitted by biting infected female phlebotomine sandflies. The implication of “the NTD road map: together towards 2030” in the infection-prone regions worldwide has curtailed morbidity to a greater extent. However, limited options in antileishmanial oral and topical drugs must decipher more therapeutically efficacious agents to cure and eradicate the disease. Methods: Virtual screening based on structure, docking, & molecular dynamics approaches were adopted to identify potential lead molecules against UvrD-like helicase of Leishmania donovani from the MCULE database. Lipinski rule of five, N/O atoms (1-15), number of rings (1-2), HBDs (4-5), and HBAs (5-10) were applied as initial filters of SBVS. AutoDock Vina and GROMACS packages were used for docking and MD simulations, respectively. Results: Initial filters of SBVS workflow yielded 93885 ligand hits out of 100 plus million investigational ligands. Following the toxicology test, 28 ligands were gotten that were additional reduced to molecules (17) when accepted done the BOILED Egg model of the ADME. Six molecules were shortlisted with zero violation compliance of drug-likeness further than Lipinski RO5 viz., Egan, Veber, Muegge, Ghose, & bioavailability score having ΔG (-6.7 to -7.4 kcalmol-1) lesser than reference inhibitor miltefosine (-4.9 kcalmol-1). The stability of MCULE-5754880195-0-2 was found to be greater than the known inhibitor and ligand molecules mentioned above.Conclusion:  MCULE-5754880195-0-2 has all therapeutic features by way of an admirable oral drug molecule & could be encouraging in Leishmaniasis prevention & treatment.Keywords: UvrD-like helicase; ADME; Leishmaniasis; MCULE database; SBVS; Docking; BOILED Egg; MD simulation; ATP-binding domain

Structure-Based Virtual Screening of Antiviral Compounds Targeting the Norovirus RdRp Protein

Background: Human noroviruses (NV) are the primary etiological organisms causing acute gastroenteritis around the world, causing severe morbidity and imposing a significant economic burden. The RNA-dependent RNA polymerase (RdRp) is essential for viral replication and could be a promising target for anti-NV therapeutics. Despite the discovery of a few NV RdRp inhibitors, the majority of these pharmaceuticals have demonstrated limited efficacy in inhibiting viral replication in cellular models.Methods: In this study, computational screening of antiviral compounds was conducted targeting the NV RdRp protein. The assessment was based on binding poses and the key residues of RdRp involved in interactions with compounds.Results: The compounds namely, Ribavirin, BMS806, Dihydromyricetin, R7935788, and LY2784544 were found to bind the RdRp protein with high affinity. Notably, these compounds displayed significantly lower binding affinities compared to the positive control, PPNDS. In addition, these compounds exhibited many RdRp protein binding residues that were also present in the PPNDS.Conclusion: The results presented here suggest that these compounds have the potential to be used as inhibitors of NV RdRp in the development of antiviral medications. Nevertheless, due to the computational nature of this study, it is imperative to do experimental validation.Keywords: Noroviruses; RdRp; Virtual screening; Antiviral Compounds 

Targeting Kaposi’s sarcoma associated herpesvirus encoded protease (ORF17) by a lysophosphatidic acid molecule for treating KSHV associated diseases

Kaposi’s sarcoma associated herpesvirus (KSHV) is causative agent of Kaposi’s sarcoma, Multicentric Castleman Disease and Pleural effusion lymphoma. KSHV-encoded ORF17 encodes a protease which cleaves -Ala-Ala-, -Ala-Ser- or -Ala-Thr-bonds. The protease plays an important role in assembly and maturation of new infective virions. In the present study, we investigated expression pattern of KSHV-encoded protease during physiologically allowed as well as chemically induced reactivation condition. The results showed a direct and proportionate relationship between ORF17 expression with reactivation time. We employed virtual screening on a large database of natural products to identify an inhibitor of ORF17 for its plausible targeting and restricting Kaposi’s sarcoma associated herpesvirus assembly/maturation. A library of 307,814 compounds of biological origin (A total 481,799 structures) has been used as a screen library. 1-oleoyl-2-hydroxy-sn-glycero-3-phospho-(1′-myo-inositol) was highly effective against ORF17 in in-vitro experiments. The screened compound was tested for the cytotoxic effect and potential for inhibiting Kaposi’s sarcoma associated herpesvirus production upon induced reactivation by hypoxia, TPA and butyric acid. Treatment of reactivated KSHV-positive cells with 1-oleoyl-2-hydroxy-sn-glycero-3-phospho-(1′-myo-inositol) resulted in significant reduction in the production of Kaposi’s sarcoma associated herpesvirus. The study identified a lysophosphatidic acid molecule for alternate strategy to inhibit KSHV-encoded protease and target Kaposi’s sarcoma associated herpesvirus associated malignancies

Case report: A novel de novo loss of function variant in the DNA-binding domain of TBX2 causes severe osteochondrodysplasia

Background: T-box family members are transcription factors characterized by highly conserved residues corresponding to the DNA-binding domain known as the T-box. TBX2 has been implicated in several developmental processes, such as coordinating cell fate, patterning, and morphogenesis of a wide range of tissues and organs, including lungs, limbs, heart, kidneys, craniofacial structures, and mammary glands.Methods: In the present study, we have clinically and genetically characterized a proband showing a severe form of chondrodysplasia with developmental delay. Whole-exome sequencing (WES), Sanger sequencing, and 3D protein modeling were performed in the present investigation.Results: Whole-exome sequencing revealed a novel nonsense variant (c.529A>T; p.Lys177*; NM_005994.4) in TBX2. 3D-TBX2 protein modeling revealed a substantial reduction of the mutated protein, which might lead to a loss of function (LOF) or nonsense-mediated decay (NMD).Conclusion: This study has not only expanded the mutation spectrum in the gene TBX2 but also facilitated the diagnosis and genetic counseling of related features in affected families

Biallelic Variants in Seven Different Genes Associated with Clinically Suspected Bardet-Biedl Syndrome

Bardet-Biedl syndrome (BBS) is a rare clinically and genetically heterogeneous autosomal recessive multi-systemic disorder with 22 known genes. The primary clinical and diagnostic features include six different hallmarks, such as rod-cone dystrophy, learning difficulties, renal abnormalities, male hypogonadism, post-axial polydactyly, and obesity. Here, we report nine consanguineous families and a non-consanguineous family with several affected individuals presenting typical clinical features of BBS. In the present study, 10 BBS Pakistani families were subjected to whole exome sequencing (WES), which revealed novel/recurrent gene variants, including a homozygous nonsense mutation (c.94C>T; p.Gln32Ter) in the IFT27 (NM_006860.5) gene in family A, a homozygous nonsense mutation (c.160A>T; p.Lys54Ter) in the BBIP1 (NM_001195306.1) gene in family B, a homozygous nonsense variant (c.720C>A; p.Cys240Ter) in the WDPCP (NM_015910.7) in family C, a homozygous nonsense variant (c.505A>T; p.Lys169Ter) in the LZTFL1 (NM_020347.4) in family D, pathogenic homozygous 1 bp deletion (c.775delA; p.Thr259Leufs*21) in the MKKS/BBS5 (NM_170784.3) gene in family E, a pathogenic homozygous missense variant (c.1339G>A; p.Ala447Thr) in BBS1 (NM_024649.4) in families F and G, a pathogenic homozygous donor splice site variant (c.951+1G>A; p?) in BBS1 (NM_024649.4) in family H, a pathogenic bi-allelic nonsense variant in MKKS (NM_170784.3) (c.119C>G; p.Ser40*) in family I, and homozygous pathogenic frameshift variants (c.196delA; p.Arg66Glufs*12) in BBS5 (NM_152384.3) in family J. Our findings extend the mutation and phenotypic spectrum of four different types of ciliopathies causing BBS and also support the importance of these genes in the development of multi-systemic human genetic disorders

Genetic advances in skeletal disorders: an overview

Genetic skeletal disorders (GSDs) are a large group of rare heterogeneous disorders characterized by abnormal development, remodeling, and growth of the human skeleton's cartilage and bones. GSDs have a high spectrum of phenotypes that range from disproportionate short stature (dwarfism) in childhood to osteoarthritis in old age. According to the latest nosology classification of skeletal dysplasias, 461 disorders under 42 groups are classified according to specific radiographic, clinical, and molecular standards. In addition, correct molecular diagnosis for these rare GSDs is important for genetic and psychological counseling and treatment. GSDs are also associated with many syndromic forms that affect other parts such as hearing, vision, neurological, pulmonary, renal, or cardiac function. This review highlights the importance of GSDs and details a few selected disorders and their management strategies. [JBCGenetics 2023; 6(1.000): 57-69

Gamma Irradiation Induced Chromosome Aberrations in Meiotic Cells of Bread Wheat (Triticum aestivum L.)

Background and Objectives: Due to the ever-increasing human population and rapid urbanization, the available agricultural land becomes limited for the production of food grains. As a result, there is an urgent need for creating genetic variability upon which improved varieties could be made. The technology of induced mutagenesis plays an essential role in inducing genetic variations among crop species where hybridization is very challenging. Therefore, the present study has been designed to assess the mutagenic impact of gamma irradiation on the cytological behaviour of T. aestivum L in M1 and M2 generation. Materials and Methods: Bread wheat seeds of selected cultivar were irradiated at BARC, Mumbai with five doses. The irradiated and non-irradiated seeds were sown under field condition with three replicates for each dose according to randomized block design to raise the M1 and M2 generations for morphological and meiotic analysis. For meiosis, immature panicles were collected in early morning and immediately fixed in carnoy’s solution for at least 24 hours. Thereafter, anthers from buds were excised and squashed in acetocarmine followed by photomicrography of suitable PMCs to estimate chromosome aberrations. Results: The results displayed a progressive elevation in the chromosomal aberrations along with a significant influence on seedling emergence, plant survival and pollen fertility. The most frequent meiotic aberrations detected include chromatin clumping, univalents and early chromosome segregations at metaphase and lagging chromosomes, chromatin bridges and chromosome clumping at anaphase/telophase while unorientation, scattering, polarity disturbances and micronuclei were also noticed. In addition, the frequency of these chromosome aberrations significantly decreased in M2 generation depicting the reclamation in genomic structure. Conclusion: The present investigation supports the discovery that gamma irradiations are very effective in creating rapid genetic variability in crop plants including Triticum aestivum which could be essentially exploited for future mutation breeding programmes. The results revealed that the higher treatment doses are toxic whereas lower doses of gamma irradiations seem quite beneficial in generating promising traits with less toxicity. In this study, the cytotoxicity has increased along with gamma irradiation doses and therefore, the genetic structure of the selected bread wheat cultivar is highly affected, which will possibly create new favorable genetic changes in the following generations that would be useful for plant breeders for its improvement

Dimethoate Induces DNA Damage and Mitochondrial Dysfunction Triggering Apoptosis in Rat Bone-Marrow and Peripheral Blood Cells

Dimethoate (DM) is an organophosphorus (OP) pesticide with wide use in the pest control. Its persistence in crops and soils could possibly cause adverse health consequences in humans as well as other non-target species. Since molecular studies confirming potential genotoxicity of DM have not been previously reported, the acute in vivo toxicological impact was evaluated in Wistar rats. Significant micronuclei induction and metaphase chromosome abnormalities in bone marrow cells exposed to three different DM doses (20, 40 and 60 mg/kg-bw) at multiple treatment durations (24, 48 and 72 h) indicated positive dose response relationship, confirming its genotoxic and cytotoxic potential. Significant mitotic index decrease was seen in dosed animals compared to vehicle control. The study used peripheral blood comet assay, indicating DM-mediated damage to DNA at all exposure levels in a time responsive manner. These assays were found to be an effective, precise, and fast technique with applied value in biomonitoring studies. Cell cycle and apoptosis along with mitochondrial membrane potential (MMP) in flow cytometric analyses confirmed DM exposure decreased MMP, affected the cell cycle, and inflicted DNA damage, which led to cellular apoptosis of leukocytes culminating into immunotoxic effects. The in silico experiments consequently augmented that DM showed acceptable binding energy value for Cyclin A2, suggesting that it could inhibit the cell cycle progression by inhibiting cyclin A2

Next-Generation Sequencing-Based Pre-Implantation Genetic Testing for Aneuploidy (PGT-A): First Report from Saudi Arabia

Recently, high-throughput next-generation sequencing (NGS)-based preimplantation genetic testing for aneuploidies techniques came into use. This technique is essential for successful embryo transfer and accomplishing pregnancy, thus reducing the time and cost of additional cycles. In this study, we describe our first experience in introducing an NGS-based preimplantation genetic testing for aneuploidy (PGT-A) service using next-generation sequencing in King Abdulaziz Medical City located in Riyadh, Saudi Arabia. Our main goal was to report the successful implementation of this new technology in clinical practice and highlight the factors that may affect the results. In total, 200 blastomere biopsies were obtained from 36 in vitro fertilization (IVF) cycles from Saudi couples suffering from prolonged infertility or recurrent embryo transfer failure. NGS-based PGT-A was performed in all embryos. The results were analyzed in five age groups, showing that aneuploidy rates increased with maternal age. Moreover, the results also showed that complex abnormal embryos with (2–5) aneuploidy are the most common type of embryos. Additionally, our data showed that chromosome 16-related abnormality was the most frequent abnormality detected among all reported abnormalities. In conclusion, our study suggests that NGS-based PGT-A is an applicable and reliable technique for routine-based embryo screening, especially for couples suffering from recurrent miscarriages or multiple embryo transfer failures

Microneedles Drug Delivery Systems for Treatment of Cancer: A Recent Update

Microneedles (MNs) are tiny needle like structures used in drug delivery through layers of the skin. They are non-invasive and are associated with significantly less or no pain at the site of administration to the skin. MNs are excellent in delivering both small and large molecules to the subjects in need thereof. There exist several strategies for drug delivery using MNs, wherein each strategy has its pros and cons. Research in this domain lead to product development and commercialization for clinical use. Additionally, several MN-based products are undergoing clinical trials to evaluate its safety, efficacy, and tolerability. The present review begins by providing bird’s-eye view about the general characteristics of MNs followed by providing recent updates in the treatment of cancer using MNs. Particularly, we provide an overview of various aspects namely: anti-cancerous MNs that work based on sensor technology, MNs for treatment of breast cancer, skin carcinoma, prostate cancer, and MNs fabricated by additive manufacturing or 3 dimensional printing for treatment of cancer. Further, the review also provides limitations, safety concerns, and latest updates about the clinical trials on MNs for the treatment of cancer. Furthermore, we also provide a regulatory overview from the “United States Food and Drug Administration” about MNs