Extensive Drug Research Articles

Association of ovarian teratoma with anti-N-methyl-D-aspartate receptor encephalitis: a case report and narrative review.

Anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis is a potentially life-threatening autoimmune disorder which is strongly associated with ovarian teratomas in young female patients. The primary aim is to highlight the importance of considering NMDAR encephalitis in the differential diagnosis of young female patients presenting with acute or subacute neuropsychiatric symptoms, especially when accompanied by ovarian teratomas. This case report and literature review detail the presentation, diagnosis, and treatment of a 35-year-old G4P3 Indigenous woman who initially presented with neuropsychiatric symptoms and fever, having a history of extensive drug and alcohol use. Misdiagnosed initially, the patient's lack of response to standard treatments led to further investigations, revealing paraneoplastic anti-NMDAR encephalitis secondary to a left ovarian teratoma. The report examines the treatment regimen followed, including prednisolone, intravenous immunoglobulin, rituximab injections, and laparoscopic bilateral salpingo-oophorectomy. This case underscores the critical need for increased clinical vigilance for anti-NMDAR encephalitis in patients, particularly young females, presenting with neuropsychiatric symptoms and potential ovarian teratomas. The literature review accompanying the case report provides valuable insights into the presentation, diagnosis, and management of this complex condition. Lastly, this study emphasised the diagnostic challenges inherent in paraneoplastic neuropsychiatric syndromes, advocating for a multidisciplinary approach in similar clinical scenarios.

Role and mechanism of the outer membrane porin LamB in T-2 mycotoxin-mediated extensive drug resistance in Escherichia coli

The influence of mycotoxins in ecological niches shared with antibiotic-resistant bacteria (ARB) remains underexplored. This study examined the impact of T-2 mycotoxin on the evolution of antibiotic resistance in Escherichia coli, highlighting the role of specific porins. Our findings revealed that exposure to 10ng/mL of T-2 toxin induced multi-drug resistant (MDR) phenotypes in three E. coli. At 10-5ng/mL, T-2 toxin caused E. coli ATCC 25922 to develop stable resistance to 13 critical antibiotics, with minimum inhibitory concentrations (MICs) increasing 16- to several thousand-fold. This resistance was linked to the downregulation of the mal gene cluster. Notably, T-2 toxin reduced membrane permeability by downregulating lamB, facilitating its own entry and reducing the intracellular accumulation of both the toxin and antibiotics, thereby enhancing resistance development. LamB mediated the XDR phenotypes in E. coli, particularly by blocking last-resort antibiotics such as cephalosporins, carbapenems, tigecycline, and colistin, complicating treatment strategies. LamB demonstrated high binding affinities for T-2 toxin and various antibiotics, with specific binding sites identified for meropenem (Arg134), imipenem (Ser148, Arg170, Lys129), ceftazidime (Phe106, Lys129), and cefepime (Tyr66, Gln267, Lys269), exhibiting binding energies of -2.93, -2.58, -2.53, and -4.3, respectively. These findings suggest that even low levels of T-2 mycotoxin pose a substantial public health risk. They underscore the urgent need to address these contaminants and open new avenues for antibiotic resistance research.

Unlocking Nitrofurantoin: Understanding Molecular Mechanisms of Action and Resistance in Enterobacterales.

Antimicrobial resistance (AMR) is a global health crisis that has already claimed millions of lives and is projected to affect millions more unless urgent action is taken. Effective control of AMR requires the correct choice and dosage of antibiotics, as well as robust surveillance and research. Understanding the mechanisms of antibiotic action and the emergence of resistance phenotypes along with their genotypes is essential. This knowledge, combined with insights into resistance prevalence and spread, empowers clinicians to propose alternative therapies. Nitrofurantoin, a 70-year-old antibiotic, remains effective for the treatment of uncomplicated lower UTIs. Preventing emergence and spread of nitrofurantoin resistant superbugs would preserve the efficacy of this antibiotic which is crucial for ongoing and future AMR efforts. Nitrofurantoin resistance evolves slowly, leading to low prevalence compared to other antibiotics. However, it is often linked with extensive drug resistance, complicating treatment outcomes. Even a minor percentage of nitrofurantoin-resistant bacteria can cause significant clinical challenges due to irreversible evolution. While detailed study of these mechanisms can guide the development of strategies to combat nitrofurantoin resistance, early detection of resistant infections is critical for saving lives. The current review aims to provide a comprehensive analysis of nitrofurantoin's mechanisms of action, resistance evolution, prevalence, and resistance prediction. Our goal is to offer valuable insights for researchers and clinicians to enhance nitrofurantoin use and address the challenges posed by AMR.

Computational Assessment of Clinical Drugs against SARS-CoV-2: Foreseeing Molecular Mechanisms and Potent Mpro Inhibitors.

The emergence of new SARS-CoV-2 variants of concern (VOC) is a propulsion for accelerated potential therapeutic discovery. SARS-CoV-2's main protease (Mpro), essential for host cell viral replication, is a pre-eminent druggable protein target. Here, we perform extensive drug re-profiling of the comprehensive Excelra database, which compiles various under-trial drug candidates for COVID-19 treatment. For mechanistic understanding, the most promising screened-out molecules with targets are subjected to molecular dynamics (MD) simulations. Post-MD analyses demonstrate Darunavir, Ponatinib, and Tomivosertib forming a stable complex with Mpro, characterized by less fluctuation of Cα atoms, smooth and stable root-mean-square deviation (RMSD), and robust contact with the active site residues. Likewise, they all have lower binding free energy with Mpro, demonstrating strong affinity. In free energy landscape profiles, the distances from His41 and Cys145 exhibit a single energy minima basin, implying their preponderance in proximity to Mpro's catalytic dyad. Overall, the computational assessment earmarks promising candidates from the Excelra database, emphasizing on carrying out exhaustive biochemical experiments along with clinical trials. The work lays the foundation for potential therapeutic interventions in treating COVID-19.

Resistance patterns, virulence determinants, and biofilm genes of multidrug-resistant Pseudomonas aeruginosa isolated from fish and fish handlers

Pseudomonas aeruginosa (P. aeruginosa) is an opportunistic bacterium that is widely distributed in aquatic environments and causes major economic losses in fish and public health hazards.This study aimed to identify the occurrence of P. aeruginosa in samples collected from fish and fish handlers, and to investigate the antimicrobial susceptibility, virulence determinants, and biofilm genes of P. aeruginosa isolates. A total of 276 samples were cross-sectionally collected from Nile tilapia (53), Golden grey mullet (52), Mediterranean horse mackerel (50), Striped red mullet (71), and fish handlers (50) at five different retail fish markets in Damietta Governorate, Egypt. Pseudomonas species (spp.) were biochemically identified in 57.9% of the total examined samples. Peudomonas aeruginosa were the most prevalent species isolated from the fish and human samples via PCR technique. Peudomonas aeruginosa isolates exhibited full resistance (100%) to tobramycin (TOB), gentamicin (CN), and colistin (CL), with a high level of susceptibility (88.5%) to imipenem (IPM) using the disk diffusion method. Most P. aeruginosa isolates (84.6%) exhibited drug resistance, with 61.5% were multidrug resistance (MDR) and 23.1% were extensive drug resistance (XDR). Most isolates had at least four virulence-associated genes (lasB, toxA, exoU, and oprL) and three biofilm genes (psIA, peIA, and lasR) by using uniplex PCR. The lasI, and rhlR Quorum Sensing (QS) genes were identified in 84.6% and 61.5% in the examined P. aeruginosa isolates, respectively. The highest mortality rate in Nile tilapia experimentally infected with P. aeruginosa isolate encoding most of virulent genes. Multivariate analyses revealed high heterogeneity among the examined isolates. This study revealed the emergence of virulent and drug resistant P. aeruginosa isolates in fish, poses high risks to consumers and food. Thus, strict hygienic measures should be considered when catching, handling, and storing fish, in addition to the routine application of antimicrobial susceptibility testing.

Effectiveness of new antituberculosis drugs in the treatment of children and adolescents with chemoresistant tuberculosis

BACKGROUND. There is a significant decrease the effectiveness of antituberculous (anti-TB) treatment on the background of multidrug and extensive drug resistance (MDR/XDR) of Mycobacterium tuberculosis. Therefore, in order to increase the effectiveness of treatment MDR-/XDR-TB a new antimycobacterial drugs such as bedaquiline (Bdq), delamanid (Dlm) and pretomanid have been introduced both for adults, children and adolescents in recent years. MATERIALS AND METHODS. On the basis of a retrospective cohort analysis of the data of patients' medical records the evaluation of the clinical effectiveness of chemotherapy with Bdq and Dlm was carried out. The main group: 40 children and adolescents with MDR-/XDR-TB of lungs, who received complex antimycobacterial therapy (AMBT) with Bdq and Dlm. The control group consisted of 27 patients who received complex AMBT without Bdq and Dlm. Age range – from 3 to 18 years. RESULTS AND DISCUSSION. On the background of AMBT during the first 3 months of treatment was established stopping bacterial secretion among all patients of main and control groups. However, in control group compare to main one stopping bacterial secretion was significant slowly (p<0.05). At the stage of completion of the intensive phase of AMBT, the normalization of immunological indicators occurred in 29.6±2.8 % of control group and in 43.4±4.5 % of main one. A significant difference between the groups among the immunoregulatory index CD3+CD4+/CD3+CD8+, IgM and circulating immune complexes was obtained. Among children and adolescents of the main group positive dynamic of immunological changes were observed 1.5 times more often. Among all patients of main group the resolution of the infiltration, consolidation of the focus and the absence of decay cavities were ascertained at the end of the anti-TB course. Anti-TB treatment with the formation of small residual changes into lung tissue ended in 77.5 % patients of main group. In 12.5 % cases of control group destructions persisted and bacterial excretion resumed. A large residual changes such as multiple dense foci, fibrosis and residual decay cavities in control group were observed 2.3 times more often (51.9 % vs 22.5 %), p<0.05, than in main one. Using Bdq and Dlm among children and adolescents with MDR-/XDR-TB significantly increased efficiency of complex treatment. Among main group (72.5 %) compare to control (33.3 %) one the results of treatment to be considered “cured” were 2.2 times more likely and 1.5 times less often – “completed” (27.5 % vs 51.8 % respectively). The success rate of treatment among children and adolescents who received Bdq and Dlm was 100.0 % and among patients without these new drugs – 85.2 %. CONCLUSIONS. The criteria used show that AMBT combined with Bdq and Dlm is 1.5-2.2 times more effective (according to a separate criterion) than AMBT without these drugs.

Prediction of structure of mycobacterial efflux pump protein Rv0194 and molecular dynamics simulation of the predicted structures

Tuberculosis is a major cause of morbidity and mortality primarily in developing nations. The rising number of cases of multidrug resistance and extensive drug resistance are a critical concern for the management of the condition. Even though new antibiotics are being developed, eventually there are also strains that are resistant to them. The evolution of resistance in Mycobacterium tuberculosis is significantly influenced by drug efflux caused by efflux pumps. Rv0194 is an important efflux pump associated with resistance to multiple drugs like beta lactam antibiotics like ampicillin and also erythromycin and novobiocin. The introduction of efflux inhibitors for Rv0194 could shorten the course of current therapy and improve the efficacy of second-line medications. Building a trustworthy molecular model of this efflux pump is the goal of this study. We created 3 models using different modeling tools. These models were then subjected to a 20 ns molecular dynamics simulation in a lipid bilayer. We find that the model built by Swiss Model shows the best results in molecular modeling and validation and the structure is also stable throughout the 20 ns MD simulations. Consequently, this model is reliable and can be used for further studies.

Serotype distribution and antimicrobial resistance of Streptococcus pneumoniae isolated from children in Japan, 2023

BackgroundThe prevalence of serotypes and antimicrobial resistance of Streptococcus pneumoniae was characterized among children thirteen years after the licensure of the pneumococcal conjugate vaccine (PCV) in Japan. MethodsA total of 353 pneumococcal isolates were collected from Japanese children between March and July 2023. All the isolates were serotyped using genetic methods and tested for susceptibility to 14 antimicrobial agents. ResultsAmong the 353 isolates, the prevalence rates of non-PCV13 and non-PCV20 serotypes were 96.9 % and 77.9 %, respectively, including the dominant non-PCV13/PCV20 serotypes 23A (16.1 %), 35B (15.3 %), 15A (10.5 %), 15C (9.3 %), and 34 (9.1 %), which accounted for 60.3 % of all isolates. The high non-susceptibility rates were observed for macrolides (erythromycin, azithromycin, and clarithromycin; ≥81.9 %) and tetracycline (80.7 %). Penicillin non-susceptibility and multidrug resistance (MDR) were detected in 49.9 % (6.8 % resistant and 43.1 % intermediate) and 68.3 % of the isolates, respectively. The three most common non-PCV13/PCV20 serotypes 15A, 23A, and 35B exhibited high prevalence rates of penicillin non-susceptibility (≥89.5 %) and MDR (≥81.5 %). Extensive drug resistance was observed in 10.5 % of all isolates belonging to six different serotypes (12F, 23A, 11A, 15A, 35B, and 15B) and in the non-encapsulated strains of S. pneumoniae. ConclusionsOur study revealed a higher prevalence of non-susceptibility to penicillin with MDR in the three most common non-PCV13/PCV20 serotypes 15A, 23A, and 35B, in Japan, suggesting their persistence in the PCV13 era.

Clinical Characteristics and Molecular Insights of Carbapenem-Resistant Klebsiella pneumoniae Isolates from Patients in Intensive Care Units.

Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP), a significant worldwide public health threat, is common in patients in intensive care units. Methods: A retrospective study was conducted over a period of 22 months to assess the risk factors associated with infection caused by CRKP isolates. Strain identification was performed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and antimicrobial sensitivity was assessed using the micro broth dilution method and Kirby-Bauer test. The genes blaKPC, blaOXA-48, blaNDM, blaVIM, and blaGES were amplified using polymerase chain reaction (PCR), followed by sequencing of the PCR products. The polymerase hypermucoviscosity phenotype was determined using the string test. Capsular serotypes (K1, K2) and presence of the virulence gene (rmpA) in positive isolates were investigated using phenotypic tests followed by PCR. Results: Length of hospitalization and use of carbapenems were associated with CRKP infection. CRKP isolates exhibited extensive drug resistance, but retained sensitivity to colistin and ceftazidime-avibactam (CZA). The main gene detected in 35 CRKP isolates was blaKPC-2. In addition, 11 strains were positive in the string test, and two of these strains carried rmpA. Conclusions: Prolonged hospitalization and carbapenem exposure increased the risk of CRKP infection in intensive care unit (ICU) patients. The prevalence of CRKP carrying the blaKPC-2 gene was high, and suspected hypervirulent carbapenem-resistant K. pneumoniae isolates were scattered.

Periodic phenotypic profile analysis of Acinetobacter baumannii drug resistance characteristics showing the emergence of PDR.

Acinetobacter baumannii, one of the ESKAPE pathogens, is on the World Health Organization (WHO) list of priorities needing urgent new effective antimicrobial agents due to exhibited high resistance by the bacterium to currently available antibiotics. This study examines the periodic changes of clinical A. baumannii isolates and their antimicrobial resistance patterns and types in Southeastern region of Saudi Arabia. One hundred and seventy-seven randomly selected A. baumannii isolates were used for the investigation with bacterial identities (IDs) and antimicrobial assay ascertained with Gram-negative (GN) ID cards and antimicrobial susceptibility test (AST) cards of Vitek 2 Compact Automated System according to manufacturer's guidelines. Descriptive phenotypic types of isolates were compared using comparison proportion and Fisher extraction test, while Morpheus versatile matrix visualization and analysis software was used for the dendrogram of hierarchical clustering. A significantly higher proportion of samples were from males compared to females (p = 0.025), with 33.33% of samples originating from patients aged 51-70 years. Resistance was high for imipenem (93%), meropenem (94%), levofloxacin, ciprofloxacin (99%), and aztreonam (98%). There was less percentage resistance to colistin (18%), tigecycline (23%), and minocycline (23%). Multidrug resistance (MDR)/carbapenem-resistant Acinetobacter baumannii (CRAB) was observed consistently across all years. There was no extensive drug resistance (XDR) among isolates from 2013 to 2014, but it was present in the 2016 to 2018 and 2019 to 2020 periods, while pandrug resistance was seen only in the 2019 to 2020 isolates. The study shows a clear trend of the isolates changing from MDR to XDR and then to pandrug resistance over the study period. Also, it indicates that carbapenems might no longer be a treatment choice in this study region. Although colistin exhibited less resistance, the toxicity of the drug reduces its usefulness. The development of pandrug resistance is a critical concern.

High-Throughput Drug Stability Assessment via Biomimetic Metalloporphyrin-Catalyzed Reactions Using Laser-Assisted Rapid Evaporative Ionization Mass Spectrometry (LA-REIMS)

Background: Building extensive drug candidate libraries as early in the development pipeline as possible, with high-throughput in vitro absorption, distribution, metabolism, and excretion (ADME) profiling, is crucial for the selection of lead compounds to guide subsequent research and production phases. Traditionally, the analysis of metabolic stability assays heavily relies on high-throughput LC-MS/MS (liquid chromatography tandem mass spectrometry) techniques to meet with the lead profiling demands. Laser-assisted rapid evaporative ionization mass spectrometry (LA-REIMS) is a quick and efficient technique for characterizing complex biological samples without laborious sample preparation. Objective: In this study, using an automated LA-REIMS well plate reader, achieving an 8 s per sample measurement time, the oxidative metabolic stability of active drug agents was assessed using biomimetic metalloporphyrin-based oxidative model reactions. Results: The results obtained using the novel LA-REIMS-based protocol were compared to and corroborated by those obtained using conventional HPLC-UV-MS (high performance liquid chromatography with ultra-violet detection coupled with mass spectrometry) measurements. Conclusions: LA-REIMS emerges as a promising technique, demonstrating potential suitability for semi-quantitative high-throughput metabolic stability in an optimized solvent environment.

In-depth comparative pathogenome, virulome, and resistome analysis of an extensive drug resistant Ralstonia mannitolilytica strain isolated from blood

IntroductionRalstonia mannitolilytica is an global opportunistic pathogen responsible for various diseases. In this study, we reported the genome of a R. mannitolilytica isolate responsible for bacteremia in an acute exacerbation of chronic obstructive pulmonary disease (AECOPD). MethodsBacterial identification was performed with a Vitek2™ Automated System and 16S rRNA sequencing with BLASTn against the Non-Redundant Protein Sequence (Nr) database. Genome sequencing and analysis were performed using PacBio RS II sequencer, Hierarchical Genome Assembly Process assembly, as well as multiple annotation databases to better understand the innate features. Antibiotic resistance genes and virulence factors were specifically identified through Antibiotic Resistance Genes database and Virulence Factors of Pathogenic Bacteria databases. ResultsThe complete genome sequence was assembled into two chromosomes with 3,495,817 bp and 1,342,871 bp in length and GC% of 65.37 % and 66.43 %, respectively. The two chromosomes were fully annotated. In chromosome 1 and 2, 19 and 14 antibiotic resistant genes and 48 and 55 virulence factors were predicted, respectively. Specifically, beta-lactam resistance genes blaOXA-443, blaOXA-444 were acquired. ConclusionsThis study aids in the understanding of the innate features of R. mannitolilytica in AECOPD.

Screening of the Pandemic Response Box library identified promising compound candidate drug combinations against extensively drug-resistant Acinetobacter baumannii

Infections caused by antimicrobial-resistant Acinetobacter baumannii pose a significant threat to human health, particularly in the context of hospital-acquired infections. As existing antibiotics lose efficacy against Acinetobacter isolates, there is an urgent need for the development of novel antimicrobial agents. In this study, we assessed 400 structurally diverse compounds from the Medicines for Malaria Pandemic Response Box for their activity against two clinical isolates of A. baumannii: A. baumannii 5075, known for its extensive drug resistance, and A. baumannii QS17-1084, obtained from an infected wound in a Thai patient. Among the compounds tested, seven from the Pathogen box exhibited inhibitory effects on the in vitro growth of A. baumannii isolates, with IC50s ≤ 48 µM for A. baumannii QS17-1084 and IC50s ≤ 17 µM for A. baumannii 5075. Notably, two of these compounds, MUT056399 and MMV1580854, shared chemical scaffolds resembling triclosan. Further investigations involving drug combinations identified five synergistic drug combinations, suggesting potential avenues for therapeutic development. The combination of MUT056399 and brilacidin against A. baumannii QS17-1084 and that of MUT056399 and eravacycline against A. baumannii 5075 showed bactericidal activity. These combinations significantly inhibited biofilm formation produced by both A. baumannii strains. Our findings highlight the drug combinations as promising candidates for further evaluation in murine wound infection models against multidrug-resistant A. baumannii. These compounds hold potential for addressing the critical need for effective antibiotics in the face of rising antimicrobial resistance.

GENETIC VARIABILITY AND GEOGRAPHIC DISTRIBUTION OF MYCOBACTERIUM TUBERCULOSIS LINEAGE 2

Mycobacterium tuberculosis (MTB) is a substantial threat to public health, infecting approximately 10 million individuals annually with tuberculosis. Among the genetic lineages of MTB, lineage 2 (L2), notably the Beijing family, plays a significant role in global tuberculosis epidemiology, accounting for nearly a quarter of all reported TB cases. Originating possibly in East Asia, this lineage spread globally, causing significant epidemics in Central Asia, Eastern Europe, and Eastern Africa. Geographic variability in the distribution of MTB L2 strains reveals diverse prevalence patterns among sublineages across different regions. L2.1 (proto-Beijing) is primarily composed of isolates originating from China, Thailand, and Vietnam, with a smaller number from Japan, Malaysia, and Indonesia. The ancestral sublineage, named L2.2.A, is mostly spread in China, Japan, and Thailand, while the modern sublineage, L2.2.M, is widespread, spanning almost the entire world. Moreover, the L2.2.M1 clade demonstrates a wide geographic spread, encompassing various countries across Asia and Australia, while other subclades of the L2.2.M2, L2.2.M3, and L2.2.M4 clades show more localized distributions across different regions. The L2.2.M4 clade comprises nine subclades, L2.2.M4.1 and L2.2.M4.2 are primarily found in Thailand, while L2.2.M4.3, L2.2.M4.6, and L2.2.M4.8 predominate in China. In South Africa, L2.2.M4.4 is the predominant subclade, whereas L2.2.M4.7 is associated with Nepalese isolates. In contrast, in regions such as Central Asia, Eastern Europe, and Russia, L2 strains, particularly the Modern Beijing sublineage, dominate. Notable examples include Europe/Russia W148 outbreak L2.2.M4.5 (B0W/148), Central Asia L2.2.M4.9 (CA), Central Asia outbreak L2.2.M4.9.1 (CAO), and Clade A L2.2.M4.9.2. Additionally, recent small clades like L2.2.M5 and L2.2.M6, originating from Vietnam, Thailand, and China, have emerged, with L2.2.M6 also detected in Kenya and South Africa. In Kazakhstan, we have identified such sublineages of L2 as CAO (n=69; 67.64%) L2.2.M4.9.1, CA (n=27; 26.47%) L2.2.M4.9, B0W/148 (n=5, 4.90%) L2.2.M4.5 and one isolate representative of a rare L2.2.M4 lineage (n =1; 0.98%). Strains of this lineage demonstrate the development of multidrug resistance (MDR) and extensive drug resistance (XDR), reflecting the emergence of resistance mechanisms against all available anti-tuberculosis drugs. In summary, M. tuberculosis lineage 2, especially the Beijing family, significantly impacts global tuberculosis epidemiology, with diverse prevalence patterns among sublineages across regions.

Anti- COVID-19 drug discovery by flavonoid derivatives: an extensive computational drug design approach.

The present study deals with the in-silico analyses of several flavonoid derivatives to explore COVID-19 through pharmacophore modelling, molecular docking, molecular dynamics, drug-likeness, and ADME properties. The initial literature study revealed that many flavonoids, including luteolin, quercetin, kaempferol, and baicalin may be useful against SARS β-coronaviruses, prompting the selection of their potential derivatives to investigate their abilities as inhibitors of COVID-19. The findings were streamlined using in silico molecular docking, which revealed promising energy-binding interactions between all flavonoid derivatives and the targeted protein. Notably, compounds 8, 9, 13, and 15 demonstrated higher potency against the coronavirus Mpro protein (PDB ID 6M2N). Compound 8 has a -7.2 Kcal/mol affinity for the protein and binds to it by hydrogen bonding with Gln192 and π-sulfur bonding with Met-165. Compound 9 exhibited a significant interaction with the main protease, demonstrating an affinity of -7.9 kcal/mol. Gln-192, Glu-189, Pro-168, and His-41 were the principle amino acid residues involved in this interaction. The docking score for compound 13 is -7.5 Kcal/mol, and it binds to the protease enzyme by making interactions with Leu-41, π-sigma, and Gln-189. These interactions include hydrogen bonding and π-sulfur. The major protease and compound 15 were found to bind with a favourable affinity of -6.8 Kcal/mol. This finding was further validated through molecular dynamic simulation for 1ns, analysing parameters such as RMSD, RMSF, and RoG profiles. The RoG values for all four of the compounds varied significantly (35.2-36.4). The results demonstrated the stability of the selected compounds during the simulation. After passing the stability testing, the compounds underwent screening for ADME and drug-likeness properties, fulfilling all the necessary criteria. The findings of the study may support further efforts for the discovery and development of safe drugs to treat COVID-19.

Identification of Potential Tryptase Inhibitors from FDA-Approved Drugs Using Machine Learning, Molecular Docking, and Experimental Validation.

This study explores the innovative use of machine learning (ML) to identify novel tryptase inhibitors from a library of FDA-approved drugs, with subsequent confirmation via molecular docking and experimental validation. Tryptase, a significant mediator in inflammatory and allergic responses, presents a therapeutic target for various inflammatory diseases. However, the development of effective tryptase inhibitors has been challenging due to the enzyme's complex activation and regulation mechanisms. Utilizing a machine learning model, we screened an extensive FDA-approved drug library to identify potential tryptase inhibitors. The predicted compounds were then subjected to molecular docking to assess their binding affinity and conformation within the tryptase active site. Experimental validation was performed using RBL-2H3 cells, a rat basophilic leukemia cell line, where the efficacy of these compounds was evaluated based on their ability to inhibit tryptase activity and suppress β-hexosaminidase activity and histamine release. Our results demonstrated that several FDA-approved drugs, including landiolol, laninamivir, and cidofovir, significantly inhibited tryptase activity. Their efficacy was comparable to that of the FDA-approved mast cell stabilizer nedocromil and the investigational agent APC-366. These findings not only underscore the potential of ML in accelerating drug repurposing but also highlight the feasibility of this approach in identifying effective tryptase inhibitors. This research contributes to the field of drug discovery, offering a novel pathway to expedite the development of therapeutics for tryptase-related pathologies.

Genomic profiling of pan-drug resistant proteus mirabilis Isolates reveals antimicrobial resistance and virulence gene landscape

Proteus mirabilis is a gram-negative pathogen that caused significant opportunistic infections. In this study we aimed to identify antimicrobial resistance (AMR) genes and virulence determinants in two pan-drug resistant isolate “Bacteria_11” and “Bacteria_27” using whole genome sequencing. Proteus mirabilis “Bacteria_11” and “Bacteria_27” were isolated from two different hospitalized patients in Egypt. Antimicrobial susceptibility determined using Vitek 2 system, then whole genome sequencing (WGS) using MinION nanopore sequencing was done. Antimicrobial resistant genes and virulence determinants were identified using ResFinder, CADR AMR database, Abricate tool and VF analyzer were used respectively. Multiple sequence alignment was performed using MAFFT and FastTree, respectively. All genes were present within bacterial chromosome and no plasmid was detected. “Bacteria_11” and “Bacteria_27” had sizes of approximately 4,128,657 bp and 4,120,646 bp respectively, with GC content of 39.15% and 39.09%. “Bacteria_11” and “Bacteria_27” harbored 43 and 42 antimicrobial resistance genes respectively with different resistance mechanisms, and up to 55 and 59 virulence genes respectively. Different resistance mechanisms were identified: antibiotic inactivation, antibiotic efflux, antibiotic target replacement, and antibiotic target change. We identified several genes associated with aminoglycoside resistance, sulfonamide resistance. trimethoprim resistance tetracycline resistance proteins. Also, those responsible for chloramphenicol resistance. For beta-lactam resistance, only blaVEB and blaCMY-2 genes were detected. Genome analysis revealed several virulence factors contribution in isolates pathogenicity and bacterial adaptation. As well as numerous typical secretion systems (TSSs) were present in the two isolates, including T6SS and T3SS. Whole genome sequencing of both isolates identify their genetic context of antimicrobial resistant genes and virulence determinants. This genomic analysis offers detailed representation of resistant mechanisms. Also, it clarifies P. mirabilis ability to acquire resistance and highlights the emergence of extensive drug resistant (XDR) and pan-drug resistant (PDR) strains. This may help in choosing the most appropriate antibiotic treatment and limiting broad spectrum antibiotic use.

Natural product-derived ALK inhibitors for treating ALK-driven lung cancers: an in silico study.

Anaplastic lymphoma kinase (ALK)-driven lung cancer represents a critical therapeutic target, demanding innovative approaches for the identification of effective inhibitors. Anaplastic lymphoma kinase (ALK), a key protein involved in the pathogenesis of ALK-driven lung cancers, has been the focus of extensive drug discovery efforts. This study employed a comprehensive computational drug discovery approach, integrating virtual screening with the Lipinski filter, re-docking, molecular dynamics (MD) simulations, and free energy calculations to identify potential inhibitors from a natural compound library. Utilizing the MTiOpenScreen web server, we screened for compounds that exhibit favorable interactions with ALK, resulting in 1227 compounds with virtual screening scores ranging from -10.2 to -3.7kcal/mol. Subsequent re-docking of three selected compounds (ZINC000059779788, ZINC000043552589, and ZINC000003594862) and one reference compound against ALK yielded docking scores -10.4, -10.2, -10.2, and -10.1kcal/mol, respectively. These compounds demonstrated promising interactions with ALK, suggesting potential inhibitory effects. Advanced analyses, including MD simulation and binding free energy calculations, further supported the potential efficacy of these compounds. MD simulations, particularly the root mean square deviation (RMSD) and root mean square fluctuation (RMSF) analyses, revealed that compounds ZINC000059779788 and ZINC000003594862 achieved better stability compared to compound ZINC000043552589. These stable conformations suggest effective binding over time. Free energy calculations using the MM/GBSA method showed that ZINC000059779788 had the most favorable binding energy, indicating a strong and stable interaction with the ALK protein. The promising computational findings from this study emphasize the necessity for additional experimental testing to verify the therapeutic efficacy of these natural compounds for treating lung cancers.

Knowledge, Attitudes and Behaviors of Academic and Administrative Staff at Izmir Bakırçay University towards Rational Drug Use

Objective: It is aimed to evaluate the knowledge level and behaviors of university staff about rational drug use, and to create literature on intervention studies. Materials and Methods: The descriptive study was carried out online among the academic and administrative staff of İzmir Bakırçay University. Its population consists of 308 university personnel and the sample was not selected. A 20-question questionnaire and a 21-item Rational Drug Use Scale were sent to all personnel who accepted the study, and 219 personnel (71.1%) participated. Independent variables, sociodemographic characteristics and substance use habits are the dependent variable scale score. SPSS 20.0 statistical package program was used. Descriptive statistics, number and percentage distributions, differences between groups were evaluated with Chi-Square and Fisher's exact tests. Results: 89.9% of the participants had good knowledge of rational drug use, and their average score was 38.4±3.5. The level of knowledge of women, academic staff and participants aged 40 and over is higher (p=0.015). Conclusion: Academic staff and female employees aged 40 and over have higher RHR knowledge levels. In order to gain Rational Drug Use behavior, both health professionals and the society should be provided with extensive training opportunities and drug policies should be developed.

Silver nanoparticle with potential antimicrobial and antibiofilm efficiency against multiple drug resistant, extensive drug resistant Pseudomonas aeruginosa clinical isolates

BackgroundThe study aims to investigate the effect of combining silver nanoparticles (AGNPs) with different antibiotics on multi-drug resistant (MDR) and extensively drug resistant (XDR) isolates of Pseudomonas aeruginosa (P. aeruginosa) and to investigate the mechanism of action of AGNPs.MethodsAGNPs were prepared by reduction of silver nitrate using trisodium citrate and were characterized by transmission electron microscope (TEM) in addition to an assessment of cytotoxicity. Clinical isolates of P. aeruginosa were collected, and antimicrobial susceptibility was conducted. Multiple Antibiotic Resistance (MAR) index was calculated, and bacteria were categorized as MDR or XDR. Minimum inhibitory concentration (MIC) of gentamicin, ciprofloxacin, ceftazidime, and AGNPs were determined. The mechanism of action of AGNPs was researched by evaluating their effect on biofilm formation, swarming motility, protease, gelatinase, and pyocyanin production. Real-time PCR was performed to investigate the effect on the expression of genes encoding various virulence factors.ResultsTEM revealed the spherical shape of AGNPs with an average particle size of 10.84 ± 4.64 nm. AGNPS were safe, as indicated by IC50 (42.5 µg /ml). The greatest incidence of resistance was shown against ciprofloxacin which accounted for 43% of the bacterial isolates. Heterogonous resistance patterns were shown in 63 isolates out of the tested 107. The MAR indices ranged from 0.077 to 0.84. Out of 63 P. aeruginosa isolates, 12 and 13 were MDR and XDR, respectively. The MIC values of AGNPs ranged from 2.65 to 21.25 µg /ml. Combination of AGNPs with antibiotics reduced their MIC by 5–9, 2–9, and 3-10Fold in the case of gentamicin, ceftazidime, and ciprofloxacin, respectively, with synergism being evident. AGNPs produced significant inhibition of biofilm formation and decreased swarming motility, protease, gelatinase and pyocyanin production. PCR confirmed the finding, as shown by decreased expression of genes encoding various virulence factors.ConclusionAGNPs augment gentamicin, ceftazidime, and ciprofloxacin against MDR and XDR Pseudomonas isolates. The efficacy of AGNPs can be attributed to their effect on the virulence factors of P. aeruginosa. The combination of AGNPs with antibiotics is a promising strategy to attack resistant isolates of P. aeruginosa.