Exploring the anti-protozoal mechanisms of Syzygium aromaticum phytochemicals targeting Cryptosporidium parvum lactate dehydrogenase through molecular dynamics simulations.

Cryptosporidium parvum (C. parvum), a protozoan parasite, is known to induce significant gastrointestinal disease in humans. Lactate dehydrogenase (LDH), a protein of C. parvum, has been identified as a potential therapeutic target for developing effective drugs against infection. This study utilized a computational drug discovery approach to identify potential drug molecules against the LDH protein of C. parvum. In the present investigation, we conducted a structure-based virtual screening of 55 phytochemicals from the Syzygium aromaticum (S. aromaticum). This process identified four phytochemicals, including Gallotannin 23, Eugeniin, Strictinin, and Ellagitannin, that demonstrated significant binding affinity and dynamic stability with LDH protein. Interestingly, these four compounds have been documented to possess antibacterial, antiviral, anti-inflammatory, and antioxidant properties. The docked complexes were simulated for 100 ns using Desmond to check the dynamic stability. Finally, the free binding energy was computed from the last 10ns MD trajectories. Gallotannin 23 and Ellagitannin exhibited considerable binding affinity and stability with the target protein among all four phytochemicals. These findings suggest that these predicted phytochemicals from S. aromaticum could be further explored as potential hit candidates for developing effective drugs against C. parvum infection. The in vitro and in vivo experimental validation is still required to confirm their efficacy and safety as LDH inhibitors.

Discovery of Bispecific Lead Compounds from Azadirachta indica against ZIKA NS2B-NS3 Protease and NS5 RNA Dependent RNA Polymerase Using Molecular Simulations.

Zika virus (ZIKV) has been characterized as one of many potential pathogens and placed under future epidemic outbreaks by the WHO. However, a lack of potential therapeutics can result in an uncontrolled pandemic as with other human pandemic viruses. Therefore, prioritized effective therapeutics development has been recommended against ZIKV. In this context, the present study adopted a strategy to explore the lead compounds from Azadirachta indica against ZIKV via concurrent inhibition of the NS2B-NS3 protease (ZIKVpro) and NS5 RNA dependent RNA polymerase (ZIKVRdRp) proteins using molecular simulations. Initially, structure-based virtual screening of 44 bioflavonoids reported in Azadirachta indica against the crystal structures of targeted ZIKV proteins resulted in the identification of the top four common bioflavonoids, viz. Rutin, Nicotiflorin, Isoquercitrin, and Hyperoside. These compounds showed substantial docking energy (-7.9 to -11.01 kcal/mol) and intermolecular interactions with essential residues of ZIKVpro (B:His51, B:Asp75, and B:Ser135) and ZIKVRdRp (Asp540, Ile799, and Asp665) by comparison to the reference compounds, O7N inhibitor (ZIKVpro) and Sofosbuvir inhibitor (ZIKVRdRp). Besides, long interval molecular dynamics simulation (500 ns) on the selected docked poses reveals stability of the respective docked poses contributed by intermolecular hydrogen bonds and hydrophobic interactions. The predicted complex stability was further supported by calculated end-point binding free energy using molecular mechanics generalized born surface area (MM/GBSA) method. Consequently, the identified common bioflavonoids are recommended as promising therapeutic inhibitors of ZIKVpro and ZIKVRdRp against ZIKV for further experimental assessment.

Structural analogs of 2-(4-fluorophenyl)-6-methyl-3-(pyridin-4-yl)pyrazolo[1,5-a]pyridine for targeting Candida albicans non-essential stress kinase Yck2 through protein-ligand binding and dynamics analysis.

The rise in drug-resistant fungal infections poses a significant public health concern, necessitating the development of new antifungal therapies. We aimed to address this challenge by targeting a yeast casein kinase of Candida albicans for antifungal drug development. The compound library contained 589 chemical structures similar to the previously identified kinase inhibitor GW461484A. Through virtual screening, four compounds with the PubChem IDs 102583821, 12982634, 102487860, and 86260205 were selected based on their binding energies. Hydrophobic bonds and van der Waals interactions stabilised the docked complexes. Comprehensive interaction studies and a 200-nanosecond molecular dynamics simulation suggested that these molecules can maintain stable interactions with the target, as evidenced by satisfactory RMSD and RMSF values. The Rg-RMSD-based Free Energy Landscape of these complexes indicated thermodynamic stability due to the presence of conformers with global minima. These promising findings highlight the potential for developing novel antifungal therapies targeting Yck2 in C. albicans. Further experimental validation is required to assess the efficacy of these compounds as antifungal agents. This research provides a significant step towards combating antifungal resistance and opens up a new avenue for drug discovery.

Comprehensive In Silico Characterization of the Coding and Non-Coding SNPs in Human Dectin-1 Gene with the Potential of High-Risk Pathogenicity Associated with Fungal Infections.

The human C-type lectin domain family 7 member A (CLEC7A) gene encodes a Dectin-1 protein that recognizes beta-1,3-linked and beta-1,6-linked glucans, which form the cell walls of pathogenic bacteria and fungi. It plays a role in immunity against fungal infections through pathogen recognition and immune signaling. This study aimed to explore the impact of nsSNPs in the human CLEC7A gene through computational tools (MAPP, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT, SNAP, and PredictSNP) to identify the most deleterious and damaging nsSNPs. Further, their effect on protein stability was checked along with conservation and solvent accessibility analysis by I-Mutant 2.0, ConSurf, and Project HOPE and post-translational modification analysis using MusiteDEEP. Out of the 28 nsSNPs that were found to be deleterious, 25 nsSNPs affected protein stability. Some SNPs were finalized for structural analysis with Missense 3D. Seven nsSNPs affected protein stability. Results from this study predicted that C54R, L64P, C120G, C120S, S135C, W141R, W141S, C148G, L155P, L155V, I158M, I158T, D159G, D159R, I167T, W180R, L183F, W192R, G197E, G197V, C220S, C233Y, I240T, E242G, and Y3D were the most structurally and functionally significant nsSNPs in the human CLEC7A gene. No nsSNPs were found in the predicted sites for post-translational modifications. In the 5' untranslated region, two SNPs, rs536465890 and rs527258220, showed possible miRNA target sites and DNA binding sites. The present study identified structurally and functionally significant nsSNPs in the CLEC7A gene. These nsSNPs may potentially be used for further evaluation as diagnostic and prognostic biomarkers.

Increased prevalence of fungemia in Medina, Saudi Arabia.

Background: The prevalence of fungal infection is increasing globally due to an increase in the immunocompromised and aging population. We investigated epidemiological changes in fungemia in one of the major centers in Medina over seven years period with 87,447 admissions. Methods: Retrospective search of records for causative agents of fungemia in inpatients at King Fahad Hospital (KFH) in 2013-2019. Fungal-positive blood cultures, demographic, and treatment data were extracted. Results: A total of 331 fungemia episodes proven by blood culture were identified in 46 patients. The annual prevalence of fungemia increased from 0.072 in 2013 to 1.546 patients per 1,000 in 2019. The mean age of fungemia episodes was 56 years, and 62% of episodes occurred in females. Samples from central blood incubated aerobically yielded the highest fungemia rate, accounting for 55% (n = 182). Among yeast species, Candida parapsilosis was responsible for the highest number of episodes 37% (n = 122), followed by Candida glabrata (32%; n = 107), Candid albicans (29%; n = 94), and Cryptococcus neoformans (1%; n = 4). Among molds, Lichtheimia (Absidia) species was the most common (1%; n = 3). Yeast-like fungi Trichosporion mucoides accounted for (0.003% n = 1). The use of antifungal treatment has increased (96%) over the years (2013-2019). An increase in resistance rate of 2% was found in C. albicans and C. glabrata. The most prevalent comorbidity was renal disease (24.2%). Conclusions: C. parapsilosis was the leading cause of fungemia. The association of renal disease with increased candidemia was alarming. This study is a fundamental resource to establish management policies for fungal infection in the region.

A multi-targeted computational drug discovery approach for repurposing tetracyclines against monkeypox virus.

Monkeypox viral infection is an emerging threat and a major concern for the human population. The lack of drug molecules to treat this disease may worsen the problem. Identifying potential drug targets can significantly improve the process of developing potent drug molecules for treating monkeypox. The proteins responsible for viral replication are attractive drug targets. Identifying potential inhibitors from known drug molecules that target these proteins can be key to finding a cure for monkeypox. In this work, two viral proteins, DNA-dependent RNA polymerase (DdRp) and viral core cysteine proteinase, were considered as potential drug targets. Sixteen antibiotic drugs from the tetracycline class were screened against both viral proteins through high-throughput virtual screening. These tetracycline class of antibiotic drugs have the ability to inhibit bacterial protein synthesis, which makes these antibiotics drugs a prominent candidate for drug repurposing. Based on the screening result obtained against DdRp, top two compounds, namely Tigecycline and Eravacycline with docking scores of - 8.88 and - 7.87 kcal/mol, respectively, were selected for further analysis. Omadacycline and minocycline, with docking scores of - 10.60 and - 7.51 kcal/mol, are the top two compounds obtained after screening proteinase with the drug library. These compounds, along with reference compounds GTP for DdRp and tecovirimat for proteinase, were used to form protein-ligand complexes, followed by their evaluation through a 300 ns molecular dynamic simulation. The MM/GBSA binding free energy calculation and principal components analysis of these selected complexes were also conducted for understanding the dynamic stability and binding affinity of these compounds with respective target proteins. Overall, this study demonstrates the repurposing of tetracycline-derived drugs as a therapeutic solution for monkeypox viral infection.

Assessing the inhibitory potential of anti-dengue compounds against Japanese encephalitis virus RNA dependent RNA polymerase: an in silico study.

Japanese encephalitis (JE), a neurological infection of severe nature, is caused by the Japanese encephalitis virus (JEV) and is transmitted by the mosquito vector. The polymerase domain of Non-structural 5 (NS5), which is also referred to as RdRp (RNA-dependent RNA polymerase), is considered a potential therapeutic target for JEV. The present study employed molecular dynamics modelling and high-throughput virtual screening to evaluate the possible antiviral activity of anti-dengue drugs against JEV RdRp. Furthermore, a ranking was performed utilising the MM/GBSA analysis to identify the three most promising compounds. Compound ID 57409246 exhibited the highest binding affinity with the protein, as evidenced by its minimum binding free energy of -72.96 kcal/mole. In contrast, the other two compounds had minimum binding free energies of -67.57 and -59.19 kcal/mole, respectively. Upon conducting a 100 nanosecond molecular dynamics simulation to confirm the binding of the chemical complexes, it was observed that the three hits, namely 57409246, 70683874, and 44577154, exhibited a consistent and stable RMSD. Subsequently, the binding strength of the trajectory was confirmed through MM/GBSA analysis. The compounds 70683874 and 57409246 exhibited the lowest binding free energies, which were -97.58 kcal/mol and -96.38 kcal/mol, respectively. The binding free energy (ΔG Bind) values for the native ligand ATP and molecule 44577154 were -65.64 kcal/mol and -69.44 kcal/mol, respectively. Overall, compared to the native ligand ATP, all three compounds exhibited higher binding affinity. The study proposes three anti-dengue molecules as a potential remedy for JE, which can be confirmed through in vitro and in vivo investigations.Communicated by Ramaswamy H. Sarma.

Investigating the Mechanism of Action of Anti-Dengue Compounds as Potential Binders of Zika Virus RNA-Dependent RNA Polymerase.

The World Health Organization (WHO) has designated the Zika virus (ZIKV) as a significant risk to the general public's health. Currently, there are no vaccinations or medications available to treat or prevent infection with the Zika virus. Thus, it is urgently required to develop a highly efficient therapeutic molecule. In the presented study, a computationally intensive search was carried out to identify potent compounds that have the potential to bind and block the activity of ZIKV NS5 RNA-dependent RNA polymerase (RdRp). The anti-dengue chemical library was subjected to high-throughput virtual screening and MM/GBSA analysis in order to rate the potential candidates. The top three compounds were then chosen. According to the MM/GBSA analysis, compound 127042987 from the database had the highest binding affinity to the protein with a minimum binding free energy of -77.16 kcal/mole. Compound 127042987 had the most stable RMSD trend and the greatest number of hydrogen bond interactions when these chemical complexes were evaluated further under a 100 ns molecular dynamics simulation. Compound 127042987 displayed the best binding free energy (GBind) of -96.50 kcal/mol, surpassing the native ligand binding energy (-66.17 kcal/mole). Thereafter, an MM/GBSA binding free energy study was conducted to validate the stability of selected chemical complexes. Overall, this study illustrated that compound 127042987 showed preferred binding free energies, suggesting a possible inhibitory mechanism against ZIKV-RdRp. As per this study, it was proposed that compound 127042987 could be used as a therapeutic option to prevent Zika virus infection. These compounds need to be tested in experiments for further validation.

Thiolation of Myco-Synthesized Fe3O4-NPs: A Novel Promising Tool for Penicillium expansium Laccase Immobilization to Decolorize Textile Dyes and as an Application for Anticancer Agent.

Environmental pollution due to the continuous uncontrolled discharge of toxic dyes into the water bodies provides insight into the need to eliminate pollutants prior to discharge is significantly needed. Recently, the combination of conventional chemotherapeutic agents and nanoparticles has attracted considerable attention. Herein, the magnetic nanoparticles (Fe3O4-NPs) were synthesized using metabolites of Aspergillus niger. Further, the surfaces of Fe3O4-NPs were functionalized using 3-mercaptoproionic acid as confirmed by XRD, TEM, and SEM analyses. A purified P. expansum laccase was immobilized onto Fe3O4/3-MPA-SH and then the developed immobilized laccase (Fe3O4/3-MPA-S-S-laccase) was applied to achieve redox-mediated degradation of different dyes. The Fe3O4/3-MPA-S-S-laccase exhibited notably improved stability toward pH, temperature, organic solvents, and storage periods. The Fe3O4/3-MPA-S-S-laccase exhibited appropriate operational stability while retaining 84.34% of its initial activity after 10 cycles. The catalytic affinity (Kcat/Km) of the immobilized biocatalyst was increased above 10-fold. The experimental data showed remarkable improvement in the dyes' decolorization using the immobilized biocatalyst in the presence of a redox mediator in seven successive cycles. Thus, the prepared novel nanocomposite-laccase can be applied as an alternative promising strategy for bioremediation of textile wastewater. The cytotoxic level of carboplatin and Fe3O4-NPs singly or in combination on various cell lines was concentration-dependent.

Pharmacophore-Model-Based Drug Repurposing for the Identification of the Potential Inhibitors Targeting the Allosteric Site in Dengue Virus NS5 RNA-Dependent RNA Polymerase.

Dengue virus (DENV) is the causative agent of DENV infection. To tackle DENV infection, the development of therapeutic molecules as direct-acting antivirals (DAAs) has been demonstrated as a truly effective approach. Among various DENV drug targets, non-structural protein 5 (NS5)-a highly conserved protein among the family Flaviviridae-carries the RNA-dependent RNA polymerase (DENVRdRp) domain at the C-terminal, and its "N-pocket" allosteric site is widely considered for anti-DENV drug development. Therefore, in this study, we developed a pharmacophore model by utilising 41 known inhibitors of the DENVRdRp domain, and performed model screening against the FDA's approved drug database for drug repurposing against DENVRdRp. Herein, drugs complying with the pharmacophore hypothesis were further processed through standard-precision (SP) and extra-precision (XP) docking scores (DSs) and binding pose refinement based on MM/GBSA binding energy (BE) calculations. This resulted in the identification of four potential potent drugs: (i) desmopressin (DS: -10.52, BE: -69.77 kcal/mol), (ii) rutin (DS: -13.43, BE: -67.06 kcal/mol), (iii) lypressin (DS: -9.84, BE: -67.65 kcal/mol), and (iv) lanreotide (DS: -8.72, BE: -64.7 kcal/mol). The selected drugs exhibited relevant interactions with the allosteric N-pocket of DENVRdRp, including priming-loop and entry-point residues (i.e., R729, R737, K800, and E802). Furthermore, 100 ns explicit-solvent molecular dynamics simulations and end-point binding free energy assessments support the considerable stability and free energy of the selected drugs in the targeted allosteric pocket of DENVRdRp. Hence, these four drugs, repurposed as potent inhibitors of the allosteric site of DENVRdRp, are recommended for further validation using experimental assays.

Glycosylated Flavonoid Compounds as Potent CYP121 Inhibitors of Mycobacterium tuberculosis.

Due to the concerning rise in the number of multiple- and prolonged-drug-resistant (MDR and XDR) Mycobacterium tuberculosis (Mtb) strains, unprecedented demand has been created to design and develop novel therapeutic drugs with higher efficacy and safety. In this study, with a focused view on implementing an in silico drug design pipeline, a diverse set of glycosylated flavonoids were screened against the Mtb cytochrome-P450 enzyme 121 (CYP121), which is established as an approved drug target for the treatment of Mtb infection. A total of 148 glycosylated flavonoids were screened using structure-based virtual screening against the crystallized ligand, i.e., the L44 inhibitor, binding pocket in the Mtb CYP121 protein. Following this, only the top six compounds with the highest binding scores (kcal/mol) were considered for further intermolecular interaction and dynamic stability using 100 ns classical molecular dynamics simulation. These results suggested a considerable number of hydrogen and hydrophobic interactions and thermodynamic stability in comparison to the reference complex, i.e., the CYP121-L44 inhibitor. Furthermore, binding free energy via the MMGBSA method conducted on the last 10 ns interval of MD simulation trajectories revealed the substantial affinity of glycosylated compounds with Mtb CYP121 protein against reference complex. Notably, both the docked poses and residual energy decomposition via the MMGBSA method demonstrated the essential role of active residues in the interactions with glycosylated compounds by comparison with the reference complex. Collectively, this study demonstrates the viability of these screened glycosylated flavonoids as potential inhibitors of Mtb CYP121 for further experimental validation to develop a therapy for the treatment of drug-resistant Mtb strains.

Production and immobilization of ß-glucanase from Aspergillus niger with its applications in bioethanol production and biocontrol of phytopathogenic fungi.

ß-Glucanase has received great attention in recent years regarding their potential biotechnological applications and antifungal activities. Herein, the specific objectives of the present study were to purify, characterize and immobilize ß-glucanase from Aspergillus niger using covalent binding and cross linking techniques. The evaluation of ß-glucanase in hydrolysis of different lignocellulosic wastes with subsequent bioethanol production and its capability in biocontrol of pathogenic fungi was investigated. Upon nutritional bioprocessing, ß-glucanase production from A. niger EG-RE (MW390925.1) preferred ammonium nitrate and CMC as the best nitrogen and carbon sources, respectively. The soluble enzyme was purified by (NH4)2SO4, DEAE-Cellulose and Sephadex G200 with 10.33-fold and specific activity of 379.1 U/mg protein. Tyrosyl, sulfhydryl, tryptophanyl and arginyl were essential residues for enzyme catalysis. The purified ß-glucanase was immobilized on carrageenan and chitosan with appreciable yield. However, the cross-linked enzyme exhibited superior activity along with remarkable improved thermostability and operational stability. Remarkably, the application of the above biocatalyst proved to be a promising candidate in liberating the associate lignocellulosic reducing sugars, which was utilized for ethanol production by Saccharomyces cerevisiae. The purified ß-glucanase revealed an inhibitory effect on the growth of two tested phytopathogens Fusarium oxysporum and Penicillium digitatum.

Updates on Molecular and Biochemical Development and Progression of Prostate Cancer.

Prostate cancer (PCa) represents the most commonly non-cutaneous diagnosed cancer in men worldwide and occupies a very wide area of preclinical and clinical research. Targeted therapy for any cancer depends on the understanding of the molecular bases and natural behaviour of the diseases. Despite the well-known effect of androgen deprivation on PCa, many patients develop resistance either for antiandrogen therapy or other new treatment modalities such as checkpoint inhibitors and chemotherapy. Comprehensive understanding of the development of PCa as well as of the mechanisms underlying its progression is mandatory to maximise the benefit of the current approved medications or to guide the future research for targeted therapy of PCa. The aim of this review was to provide updates on the most recent mechanisms regarding the development and the progression of PCa. According to the current understanding, future treatment strategies should include more predictive genetic and biomarker analysis to assign different patients to the expected most appropriate and effective treatment.