Exploring Nocardia's ecological spectrum and novel therapeutic frontiers through whole-genome sequencing: unraveling drug resistance and virulence factors.

Nocardia farcinica is the leading pathogen responsible for nocardiosis, a life-threatening infection primarily affecting immunocompromised patients. In this study, the genomic sequence of a clinically isolated N. farcinica sample was sequenced. Subsequently, the assembled genome was annotated to identify antimicrobial resistance and virulence genes, as well as plasmid and prophages. The analysis of the entire genome size was 6,021,225 bp, with a GC content of 70.78% and consists of 103 contigs and N50 values of 292,531 bp. The genome analysis revealed the presence of several antimicrobial resistance genes, including RbpA, mtrA, FAR-1, blaFAR-1, blaFAR-1_1, and rox. In addition, virulence genes such as relA, icl, and mbtH were also detected. The present study signifies that N. farcinica genome is pivotal for the understanding of antimicrobial resistance and virulence genes is crucial for comprehending resistance mechanism, and developing effective strategies to combat bacterial infections effectively, especially adhesins and toxins. This study aids in identifying crucial drug targets for combating multidrug-resistant N. farcinica in the future.

Structural and functional characterization of 6-phosphogluconate dehydrogenase in Plasmodium falciparum (3D7) and identification of its potent inhibitors.

The malarial parasite Plasmodium falciparum predominantly causes severe malaria and deaths worldwide. Moreover, resistance developed by P. falciparum to frontline drugs in recent years has markedly increased malaria-related deaths in South Asian Countries. Ribulose 5-phosphate and NADPH synthesized by Pentose Phosphate Pathway (PPP) act as a direct precursor for nucleotide synthesis and P. falciparum survival during oxidative challenges in the intra-erythrocytic growth phase . In the present study, we have elucidated the structure and functional characteristics of 6-phosphogluconate dehydrogenase (6PGD) in P. falciparum and have identified potent hits against 6PGD by pharmacophore-based virtual screening with ZINC and ChemBridge databases. Molecular docking and Molecular dynamics simulation, binding free energies (MMGBSA & MMPBSA), and Density Functional Theory (DFT) calculations were integratively employed to validate and prioritize the most potential hits. The 6PGD structure was found to have an open and closed conformation during MD simulation. The apo form of 6PGD was found to be in closed conformation, while a open conformation attributed to facilitating binding of cofactor. It was also inferred from the conformational analysis that the small domain of 6PGD has a high influence in altering the conformation that may aid in open/closed conformation of 6PGD. The top three hits identified using pharmacophore hypotheses were ChemBridge_11084819, ChemBridge_80178394, and ChemBridge_17912340. Though all three hits scored a high glide score, MMGBSA, and favorable ADMET properties, ChemBridge_11084819 and ChemBrdige_17912340 showed higher stability and binding free energy. Moreover, these hits also featured stable H-bond interactions with the active loop of 6PGD with binding free energy comparable to substrate-bound complex. Therefore, the ChemBridge_11084819 and ChemBridge_17912340 moieties demonstrate to have high therapeutic potential against 6PGD in P. falciparum.Communicated by Ramaswamy H. Sarma.

Computational screening of potential inhibitors targeting MurF of Brugia malayi Wolbachia through multi-scale molecular docking, molecular dynamics and MM-GBSA analysis.

Lymphatic filariasis is a parasitic disease caused by the worms Wuchereria bancrofti, Brugia malayi and Brugia timori. Three anti-filarial drugs namely Diethylcarbamazine, Ivermectin and Albendazole and their combinations are used as the control strategies for filariasis. The disease has received much attention in drug discovery due to the unavailability of vaccines and the toxic pharmaceutical properties of the existing drugs. In Wolbachia endosymbiont Brugia malayi, the UDP-N-acetylmuramoyl-tripeptide-d-alanyl-d-alanine ligase (MurF) plays a key role in peptidoglycan biosynthesis pathway and therefore can be considered as effective drug target against filariasis disease. Therefore, in the present study, MurF was selected as the therapeutic target to identify specific inhibitors against filariasis. Homology modeling was performed to predict the three-dimensional structure of MurF due to the absence of the experimental structure. Further molecular dynamics simulation and structure-based high throughput virtual screening with three different chemical databases (Zinc, Maybridge and Specs) were carried out to identify potent inhibitors and also to check their conformations inside the binding site of MurF, respectively. Top three compounds with high docking score and high relative binding affinity against MurF were selected. Further, validation studies, including predicted ADME (Absorption, Distribution, Metabolism, Excretion) assessment, binding free energy using MM-GBSA (Molecular Mechanics Generalized Born Surface Area) and DFT (Density Functional Theory) calculations were performed for the top three compounds. From the results, it was observed that all the three compounds were predicted to show high reactivity, acceptable range of pharmacokinetic properties and high binding affinity with the drug target MurF. Overall, the results could provide more understanding on the inhibition of MurF enzyme and the screened compounds could lead to the development of new specific anti-filarial drugs.

Computational Investigation of Increased Virulence and Pathogenesis of SARS-CoV-2 Lineage B.1.1.7

New variants of SARS-CoV-2 are being reported worldwide. More specifically, the variants reported in South Africa (501Y.V2) and United Kingdom (B.1.1.7) were found to be more contagious than the wild type. There are also speculations that the variants might evade the host immune responses induced by currently available vaccines and develop resistance to drugs under consideration. The first step of viral infection in COVID-19, occurs through the interaction of receptor binding domain (RBD) of the spike protein with peptidase domain of the human ACE-2 (hACE-2) receptor. So, possibly the mutations in the RBD domain of spike protein in the new variants could modulate the protein-protein interaction with hACE-2 receptor leading to the increased virulence. In this study, we aim to get molecular level understanding into the mechanism behind the increased infection rate due to such mutations in these variants. We have computationally studied the interaction of the spike protein in both wild-type and B.1.1.7 variant with hACE-2 receptor using combined molecular dynamics and binding free energy calculations using molecular mechanics-Generalized Born surface area (MM-GBSA) approach. The binding free energies computed using configurations from minimization run and low temperature simulation show that mutant variant of spike protein has increased binding affinity for hACE-2 receptor (i.e. {Delta}{Delta}G(N501Y,A570D) is in the range -20.4 to -21.4 kcal/mol)The residue-wise decomposition analysis and intermolecular hydrogen bond analysis evidenced that the N501Y mutation has increased interaction between RBD of spike protein with ACE-2 receptor. We have also carried out calculations using density functional theory and the results evidenced the increased interaction between three pairs of residues (TYR449 (spike)-ASP38 (ACE-2), TYR453-HIE34 and TYR501-LYS353) in the variant that could be attributed to its increased virulence. The free energies of wild-type and mutant variants of the spike protein computed from MM-GBSA approach suggests that latter variant is stable by about -10.4 kcal/mol when compared to wild type suggesting that it will be retained in the evolution due to increased stability. We demonstrate that with the use of the state-of-the art of computational approaches, we can in advance predict the more virulent nature of variants of SARS-CoV-2 and alert the world health-care system.

Structural and functional insights of STAT2-NS5 interaction for the identification of NS5 antagonist - An approach for restoring interferon signaling.

Dengue is a mosquito-borne viral infection caused by Dengue virus (DENV) and is an emerging concern in public health affecting billions of people worldwide annually with no effective drugs available till now. Immunogenic and highly conserved properties of Non-Structural Protein 5(NS5) in DENV makes it a potent marker to identify DENV infection. DENV interfere in the innate immune signaling and thereby decreases antiviral responses and favors viral replication. Viral recognition by host pathogen recognition receptors facilitates binding of interferon (IFN) to the interferon receptors that further activates both the Signal Transducer and Activator of Transcription-2 (STAT-2) a factor producing an antiviral response. The most debilitating factor of DENV infection is emaciation of human immune system by DENV- NS5. NS5 counters the antiviral response by STAT2 degradation impeding the transcriptional activation of interferon stimulated genes through interferon stimulated response elements. The present study aims to identify inhibitors for NS5 Methyl Transferase (MTase) domain and to provide an insight into the mechanism of STAT2 degradation in the host infected with DENV. Virtual screening and molecular docking studies identified five potential inhibitors ZINC84154300, ZINC08762321, ZINC08762323, ZINC12659408 and ZINC12285470 with docking scores of -10.55, -10.53, -10.78, -11.28 and -10.78 kcal/mol respectively. To further investigate the stability of the complexes, we have used Molecular Dynamics Simulations (MD). Besides, the binding free energy of top 5 docked ligands were estimated through Molecular Mechanics Generalized Born and Surface Area Solvation (MM/GBSA) methods. This study also provides an insight on the mechanism of immunological processes involved in alleviating the antiviral immune response and computational identification of potent inhibitors for viral NS5 protein.

Erratum: Stroke Epidemiology in South, East, and South-East Asia: A Review / 대한뇌졸중학회지

On page 287, “The lowest rates are observed in Japan (43.4/1,000,000 person-years and Singapore (47.9/100,000 person-years), followed by Bangladesh, Papua New Guinea, and Bhutan.” sentence should be corrected.

Green synthesized nickel nanoparticles for targeted detection and killing of S. typhimurium.

Simple and sensitive colorimetric immunosensor based on peroxidase mimetic activity and photothermal effect of nickel oxide nanoparticle (NiOGs) has been developed to detect and kill food borne pathogen Salmonella typhimurium. NiOGs showed superior peroxidase mimetic activity for oxidation of peroxidase substrate 3, 3', 5, 5'-tetramethylbenzidine (TMB). Oxidation of TMB by NiOGs followed Michaelis-Menten kinetics with Km and Vmax values of 0.25mM and 2.64×10-8M/s respectively. NiOGs was coated with citric acid (CA-NiOGs) followed by conjugation with antibody (anti-S. typhimurium) (Ab-CA-NiOGs) that effectively captured S. typhimurium. Colorimetric detection of S. typhimurium by Ab-CA-NiOGs showed a linear relationship between pathogen concentration (1×101 to 1×106cfu/mL) and color signal (652nm) with limit of detection (LOD) of 10cfu/mL. The proposed method showed no cross reactivity against other pathogens. Recovery of S. typhimurium in milk and juice samples was found to be 95 to 100% and 92 to 99% respectively. NiOGs exposed to laser irradiation showed dose dependent increase in temperature and singlet oxygen within 5min. Bacteria bound to Ab-CA-NiOGs after laser irradiation, induced membrane damage and reduced bacterial viability to 6%. The bifunctional peroxidase-mimetic activity and photothermal effect of NiOGs can be exploited in selective sensing and killing of target pathogens respectively in food products.

Stroke Epidemiology in South, East, and South-East Asia: A Review / 대한뇌졸중학회지

Asia, which holds 60% of the world’s population, comprises some developing countries which are in economic transition. This paper reviews the epidemiology of stroke in South, East and South-East Asia. Data on the epidemiology of stroke in South, East, and South-East Asia were derived from the Global Burden of Disease study (mortality, disability-adjusted life-years [DALYs] lost because of stroke), World Health Organization (vascular risk factors in the community), and publications in PubMed (incidence, prevalence, subtypes, vascular risk factors among hospitalized stroke patients). Age- and sex-standardized mortality is the lowest in Japan, and highest in Mongolia. Community-based incidence data of only a few countries are available, with the lowest rates being observed in Malaysia, and the highest in Japan and Taiwan. The availability of prevalence data is higher than incidence data, but different study methods were used for case-finding, with different age bands. For DALYs, Japan has the lowest rates, and Mongolia the highest. For community, a high prevalence of hypertension is seen in Mongolia and Pakistan; diabetes mellitus in Papua New Guinea, Pakistan, and Mongolia; hypercholesterolemia in Japan, Singapore, and Brunei; inactivity in Malaysia; obesity in Brunei, Papua New Guinea, and Mongolia; tobacco smoking in Indonesia. Hypertension is the most frequent risk factor, followed by diabetes mellitus and smoking. Ischemic stroke occurs more frequently than hemorrhagic stroke, and subarachnoid hemorrhages are uncommon. There are variations in the stroke epidemiology between countries in South, East, and South-East Asia. Further research on stroke burden is required.