Identification of potential inhibitors for Klebsiella pneumoniae carbapenemase-3: a molecular docking and dynamics study

Human vaccine candidates for infections caused by Klebsiella pneumoniae: A systematic review

Background and Aims

There are many difficulties in treating Klebsiella pneumoniae, necessitating the creation of more preventative/therapeutic measures like vaccinations. However, after numerous attempts, there is still no authorized and widely accessible vaccine. The present study aimed to systematically review published studies on K. pneumoniae vaccines in human subjects/samples.

Methods

To find published studies, several electronic databases, including Scopus, PubMed, Web of Science, ClinicalKey, ClinicalTrials.gov, and Cochrane Library were searched without time limitation using the appropriate keywords. Studies were scrutinized, and the information from those that met our inclusion criteria was gathered and analyzed.

Results

In total, 691 studies were found, of which 14 articles were included for systematic review. Bacterial lysate containing K. pneumoniae was the most studied vaccine candidate. As the main indicator of human immune responses to K. pneumoniae, antibody responses were determined by most studies. The antigen amount, the route of immunization, and the immunization schedule were varying in the studies and were chosen based on several factors such as the disease model, the vaccine type, the vaccination setting (prophylactic or therapeutic), and so on.

Conclusion

The majority of studies asserted that their vaccination was efficient and safe, which was demonstrated by a decrease in the rate of infections and the induction of protective antibody, cell-dependent, and/or cytokine responses. Altogether, the information provided here will help researchers examine the K. pneumoniae vaccine candidates more closely and take future actions that will be more consistently successful.

Performance comparison of BD Phoenix CPO detect panel with Cepheid Xpert Carba-R assay for the detection of carbapenemase-producing Klebsiella pneumoniae isolates

BACKGROUND

We aimed to compare the performance of carbapenemase classification in carbapenem-resistant Klebsiella pneumoniae (CRKP) obtained using the BD Phoenix CPO Detect panel (CPO panel) and Cepheid Xpert Carba-R assays. We analyzed 55 CRKP strains from clinical specimens collected between November 2020 and November 2022. The CPO panel was used to detect both antibiotic susceptibility and phenotypic carbapenemase classes, while Xpert Carba-R was employed to identify KPC, NDM, VIM, OXA-48, and IMP genes. Due to the limited availability of molecular kits, we arbitrarily selected 55 isolates, identified as carbapenemase-producing according to the CPO panel and with meropenem minimum inhibitory concentration values > 8 mg/L.

RESULTS

According to the Xpert Carba-R assay, 16 of the 55 isolates (29.1%) were categorised as Ambler Class A (11 of which matched CPO panel Class A identification); three isolates (5.5%) were identified as Class B and 27 isolates (49.1%) as Class D (in both cases consistent with CPO panel B and D classifications). A further eight isolates (14.5%) exhibited multiple carbapenemase enzymes and were designated as dual-carbapenemase producers, while one isolate (1.8%) was identified as a non-carbapenemase-producer. The CPO panel demonstrated positive and negative percent agreements of 100% and 85.7% for Ambler Class A, 100% and 100% for Class B, and 96.4% and 100% for Class D carbapenemase detection, respectively.

CONCLUSION

While the CPO panel's phenotypic performance was satisfactory in detecting Class B and D carbapenemases, additional confirmatory testing may be necessary for Class A carbapenemases as part of routine laboratory procedures.

In Silico Interactions of Natural and Synthetic Compounds with Key Proteins Involved in Alzheimer's Disease: Prospects for Designing New Therapeutics Compound

Memory impairment is a result of multiple factors including amyloid-beta (Aβ) accumulation. Several receptors are mediated for Aβ transport and signaling. Moreover, blood lipids are involved in Aβ signaling pathway through these receptors. Mediated blood lipid level by statins aims to regulate Aβ signaling cascade. First, the structure of receptors was taken from the RCSB PDB database and prepared with MGLTools and AutoDock tool 4. Second, the ligand was prepared for docking through AutoDock Vina. The binding affinity was calculated, and the binding sites were determined through LigPlot+ software. Besides, pharmacokinetic properties were calculated through multiple software. Finally, a molecular dynamics (MD) simulation was conducted to evaluate ligands stability along with clustering analysis to evaluate proteins connection. Our molecular docking and dynamic analyses revealed silymarin as a potential inhibitor of acetylcholinesterase (AChE), P-glycoprotein, and angiotensin-converting enzyme 2 (ACE2) with 0.704, 0.85, and 0.83 Å for RMSD along with -114.27, -107.44, and -122.51 kcal/mol for free binding energy, respectively. Moreover, rosuvastatin and quercetin have more stability compared to silymarin and donepezil in complex with P-glycoprotein and ACE2, respectively. Eventually, based on clustering and pharmacokinetics analysis, silymarin, rosuvastatin, and quercetin are suggested to be involved in peripheral clearance of Aβ. The bioactivity effects of mentioned statins and antioxidants are predicted to be helpful in treating memory impairment in Alzheimer's disease (AD). Nevertheless, mentioned drug effect could be improved by nanoparticles to facilitate penetration of the blood-brain barrier (BBB).

Nrf2-regulated antioxidant response ameliorating ionizing radiation-induced damages explored through in vitro and molecular dynamics simulations

This study aims to investigate the mechanism of natural antioxidant ferulic acid (FA) in reducing oxidative stress followed by its inhibitory effect on the Keap1-Nrf2 complex. FA was treated ex vivo with human blood for 30 min at 37 °C ± 1 °C and exposed to 1.5 Gy of γ- rays of 60Co (0.789 Gy/min) and allowed for repair for an hour at 37 °C ± 1 °C. FA's free radical scavenging capacity was measured using 2,7-dichlorofluorescein diacetate assay and cytogenetic assays. Further, a possible mechanism of protein-ligand interaction between FA and Keap1-Nrf2 pathway protein as a cellular drug target was studied using docking and molecular dynamics simulation. The 1.5 Gy of γ- rays exposed to pre-treated blood with FA showed a significant (p < 0.05) reduction in reactive oxygen species and DNA damage compared to the normal control blood group sample. The ligand-protein transient binding interaction in molecular dynamic simulation over a period of 100 ns was consistent and stable emphasizing complementary charge between the protein and ligand, speculating higher hydrophobic amino acid residues in the Keap1 active pocket. This might sway the Keap1 from interaction with Nrf2, and could lead to nuclear translocation of Nrf2 during radiation-induced oxidative stress. The present study emphasizes the radioprotective effect of FA against 1.5 Gy of γ- rays exposed to human blood and the application of in silico approaches helpful for the possible protective effect of FA.Communicated by Ramaswamy H. Sarma.

Klebsiella pneumoniae vaccine studies in animal models

The treatment of Klebsiella pneumoniae is faced with challenges demanding the development of a vaccination strategy. However, no approved and globally available vaccine exists yet. This study aimed to systematically review all published data on K. pneumoniae vaccines in animal models. Without time restrictions, electronic databases were searched using appropriate keywords. The retrieved studies were screened and the data of those that matched our inclusion criteria were collected and analyzed. In total, 2027 records were retrieved; of which 35 studies were included for systematic review. The most frequently used animal model was BALB/c mice. Proteins, polysaccharides, and their combinations (conjugates) were the most common vaccine candidates used. The amount of antigen, the route used for immunization, and the challenge strategy was varying in the studies and were chosen based on several factors such as the animal model, the type of antigen, and the schedule of immunization. Almost all studies claimed that their vaccine was effective/protective, indicated by increasing survival rate, reducing organ bacterial load, and eliciting protective antibody and/or cytokine responses. Altogether, the information presented here will assist researchers to have a better look at the K. pneumoniae vaccine candidates and to take more effective steps in the future.

Epigallocatechin gallate inhibits Francisella tularensis growth and suppresses the function of DNA-binding protein HU

Francisella tularensis is a highly infectious intracellular bacterium causing tularemia disease and is regarded as a potential biological weapon. The development of a vaccine, effective treatment, or prophylactic substances targeted against tularemia is in the forefront of interest and could help to prevent or mitigate possible malevolent acts by bioterrorism utilizing F. tularensis. The viability of F. tularensis, and thus of a tularemia disease outbreak, might potentially be suppressed by simple commonly available natural substances. Epigallocatechin gallate (EGCG) is contained in green tea and its antimicrobial effect has been described. Here, we show that EGCG can suppress F. tularensis growth and is able to reduce the bacterium's ability to replicate inside mouse bone marrow-derived macrophages (BMMs) without side effects on BMMs' own viability. We suggest one (but not the only) mechanism of EGCG action. We demonstrate that EGCG can block the main functions of HU protein, the important regulator of F. tularensis virulence, leading to overall attenuation of F. tularensis viability. EGCG can delay death of mice infected by F. tularensis and can be used as a prophylactic agent against tularemia disease. Postponing death by up to 2 days can provide sufficient opportunity to administer another treatment agent.

Computational and Preclinical Prediction of the Antimicrobial Properties of an Agent Isolated from Monodora myristica: A Novel DNA Gyrase Inhibitor

The African nutmeg (Monodora myristica) is a medically useful plant. We, herein, aimed to critically examine whether bioactive compounds identified in the extracted oil of Monodora myristica could act as antimicrobial agents. To this end, we employed the Schrödinger platform as the computational tool to screen bioactive compounds identified in the oil of Monodora myristica. Our lead compound displayed the highest potency when compared with levofloxacin based on its binding affinity. The hit molecule was further subjected to an Absorption, Distribution, Metabolism, Excretion (ADME) prediction, and a Molecular Dynamics (MD) simulation was carried out on molecules with PubChem IDs 529885 and 175002 and on three standards (levofloxacin, cephalexin, and novobiocin). The MD analysis results demonstrated that two molecules are highly compact when compared to the native protein; thereby, this suggests that they could affect the protein on a structural and a functional level. The employed computational approach demonstrates that conformational changes occur in DNA gyrase after the binding of inhibitors; thereby, this resulted in structural and functional changes. These findings expand our knowledge on the inhibition of bacterial DNA gyrase and could pave the way for the discovery of new drugs for the treatment of multi-resistant bacterial infections.

Phytochemical analysis and evaluation of antibacterial activity of Moringa oleifera extracts against gram-negative bacteria: an in vitro and molecular docking studies

Moringa oleifera seed and leaf are used traditionally for the treatment of various health problems (among others, hypertension, scrapes, skin infection, diabetes, genitourinary illnesses), and to boost the immune system, as well as to act as a contraceptive. In this study, the antibacterial activity of seed and leaf M. oleifera extracts on three-gram negative bacteria was investigated, and phytochemical analysis for the association of antibacterial activity with the active constituents in the plant was determined. Moreover, understanding of the mechanism of action was achieved by applying the Auto Dock Vina technique. The phytochemical screening of M. oleifera seed and leaf extracts exhibited the presence of alkaloids, carbohydrates, cardioactive glycosides, flavonoids, tannins, phenols, steroids and terpenoids. In silico results revealed that compounds (4-O-caffeoyl quinic acid, 4-(α-L-rhamnopyranosyloxyl)-benzylisothiocyanate); (Isoquercitrin, 4-(α-L-rhamnopyranosyloxy) benzyl glucosinolate); and (Astragalin, 4-(α-L-rhamnopyranosyloxy) benzyl glucosinolate) from leaf and seed have the highest binding affinity and very good interactions with Transcriptional Activator Protein (LasR), Klebsiella pneumoniae carbapenemase (KPC), and Malonyl-CoA-acyl carrier protein transacylase (FabD), respectively.

Molecular docking studies and biological evaluation of isoxazole-carboxamide derivatives as COX inhibitors and antimicrobial agents

Non-steroidal anti-inflammatory drugs (NSAIDs) are considered one of the most commonly used medications globally. Seventeen isoxazole-containing compounds with various functional groups were evaluated in this work to identify which one was the most potent and which group was most selective toward COX-1 and COX-2 by using an in vitro COX inhibition assay kit. Their cytotoxicity was evaluated on the normal hepatic cell line (LX-2) utilizing the MTS assay. Moreover, these molecules' antibacterial and antifungal activities were evaluated using a microdilution assay against several bacterial and fungal species. In addition, molecular docking studies were conducted to identify the possible binding interactions between these compounds and their biological targets by using the X-ray crystal structure of the human COX enzyme and different proteins of bacterial and fungal strains. At the same time, the QiKProp module was used for ADME-T analysis. The results showed that all evaluated isoxazole derivatives showed moderate to potent activities against COX enzymes. The most potent compound against COX-1 and COX-2 enzymes was A13, with IC50 values of 64 and 13 nM, respectively, and a significant selectivity ratio of 4.63. It was clear that the 3,4-dimethoxy substitution on the first phenyl ring and the Cl atom on the other phenyl pushed the 5-methyl-isoxazole ring toward the secondary binding pocket and created the ideal binding interactions with the COX-2 enzyme in comparison with the other compounds. Compound A8 showed antibacterial and antifungal activities against Pseudomonas aeruginosa, Klebsiella pneumonia, and Candida albicans with MIC values of 2 mg/ml. In fact, this compound showed possible binding interactions with the elastase in P. aeruginosa and KPC-2 carbapenemase in K. pneumonia. Furthermore, for better understanding, molecular dynamics simulations were undertaken to study the change in dynamicity of the protein backbone and ligand after the ligand binds to the protein and to ensure the stability of ligand-protein complexes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03408-8.

Molecular dynamics simulations reveal the inhibitory mechanism of Withanolide A against α-glucosidase and α-amylase

Diabetes mellitus (DM) is a global chronic disease characterized by hyperglycemia and insulin resistance. The unsavory severe gastrointestinal side-effects of synthetic drugs to regulate hyperglycemia have warranted the search for alternative treatments to inhibit the carbohydrate digestive enzymes (e.g. α-amylase and α-glucosidase). Certain phytochemicals recently captured the scientific community's attention as carbohydrate digestive enzyme inhibitors due to their low toxicity and high efficacy, specifically the Withanolides-loaded extract of Withania somnifera. That said, the present study evaluated in silico the efficacy of Withanolide A in targeting both α-amylase and α-glucosidase in comparison to the synthetic drug Acarbose. Protein-ligand interactions, binding affinity, and stability were characterized using pharmacological profiling, high-end molecular docking, and molecular-dynamic simulation. Withanolide A inhibited the activity of α-glucosidase and α-amylase better, exhibiting good pharmacokinetic properties, absorption, and metabolism. Also, Withanolide A was minimally toxic, with higher bioavailability. Interestingly, Withanolide A bonded well to the active site of α-amylase and α-glucosidase, yielding the lowest binding free energy of -82.144 ± 10.671 kcal/mol and -102.1043 ± 11.231 kcal/mol compared to the Acarbose-enzyme complexes (-63.220 ± 13.283 kcal/mol and -82.148 ± 10.671 kcal/mol). Hence, the findings supported the therapeutic potential of Withanolide A as α-amylase and α-glucosidase inhibitor for DM treatment.Communicated by Ramaswamy H. Sarma.

Receptor based virtual screening of potential novel inhibitors of tigar [TP53 (tumour protein 53)-induced glycolysis and apoptosis regulator

TP53 (tumor protein 53)-induced glycolysis and apoptosis regulator (TIGAR) belongs to the phosphatases family of proteins that modulates the level of reactive oxygen species in tumor cells. This protein plays a vital role as a negative regulator of glycolysis, thus lowering ROS levels in the cells, which helps the cancerous cells to resist programmed cell death. Besides, TIGAR also mediates the DNA damage repair in cancer cells by increasing tumor cell survival. In the current study, we have screened natural products that compete with the substrate to bind to the active site of TIGAR. Extra precision and MMGBSA scoring function were used to screen the lead molecules. Five compounds were considered as lead molecules with 2-(2-(3,4-dihydroxy phenyl)-3,5-dihydroxy-8-(4-hydroxyphenyl)-4-oxo-4H-furo[2,3-h]chromen-9-yl) acetic acid(DDFA) as a top lead with a docking score of -9.428, and -53.16 MMGBSA, bind to the positively charged amino acids present in the active site. Further, the molecular dynamics simulation studies indicated the structural stability attained by TIGAR protein upon the binding of DDFA, suggesting it to be a potent inhibitor of TIGAR, and could be employed as an anticancer drug during combinational therapy.

Recent strategies for inhibiting multidrug-resistant and β-lactamase producing bacteria: A review

β-lactam antibiotics are one of the most commonly used drugs for treating bacterial infections, but their clinical effectiveness has been severely affected with bacteria developing resistance against their action. Production of β-lactamase enzymes by bacteria that can degrade β-lactams is the most common mechanism of acquiring such resistance, leading to the emergence of multiple-drug resistance in them. Therefore, the development of efficient approaches to combat infections caused by β-lactamase producing and multidrug-resistant bacteria is the need of the hour. The present review attempts to understand such recent strategies that are in line for development as potential alternatives to conventional antibiotics. We find that apart from efforts being made to develop new antibiotics, several other approaches are being explored, which can help tackle infections caused by resistant bacteria. This includes the development of plant-based drugs, antimicrobial peptides, nano-formulations, bacteriophage therapy, use of CRISPR-Cas9, RNA silencing and antibiotic conjugates with nanoparticles of antimicrobial peptides. The mechanism of action of these novel approaches and potential issues limiting their translation from laboratory to clinics is also discussed. The review is important from an interesting knowledge base which can be useful for researchers working in this domain.

Understanding the binding conformation of ceftolozane/tazobactam with Metallo-β-lactamases VIM-5 and IMP-7 of Pseudomonas aeruginosa: A molecular docking and virtual screening process

Pseudomonas aeruginosa (P. aeruginosa) is one of the community-acquired and healthcare-associated infections causing organisms. It has become resistant to most of the available antibiotics and is termed multi-drug resistance (MDR). There are a limited number of antibiotics are available to treat such MDR organism causing infections. The ceftolozane/tazobactam is one among the combination drug therapy (CDT) prescribed for the treatment of MDR causing infections. The resistance for the same CDT was observed in the MDR P. aeruginosa harboring VIM-5 and IMP-7 Metallo beta (β)-lactamases (MBLs). To explore the resistance mechanism at the molecular level, docking studies were carried out for antibiotics against VIM-5 and IMP-7 MBLs. The Zn2 metal ions carry out the nucleophile attack on the carbonyl carbon of the β-lactam ring along with conserved water molecules. To find lead compounds against the MBLs, a virtual screening process was carried out. We have employed MODELLER for structure modeling, AutoDock for molecular docking and AutoDock Vina, Molinspiration, PASS prediction & admetSAR in virtual screening. The search of low binding energy ceftolozane analogs against VIM-5 and IMP-7 MBLs has resulted in the ZINC000029060075 and ZINC000009163636 analogs. Similarly, the screening of high binding energy inhibitors against VIM-5 and IMP-7 MBLs has resulted in ZINC000003831503 and ZINC000000897247 tazobactam analogs respectively. The ADMET prediction results in the non-toxicity of the lead compounds. Our study may provide new insights for the scientist who are designing novel drugs against MDR P. aeruginosa causing infections.

Antibacterial and COX-2 Inhibitory Tetrahydrobisbenzylisoquinoline Alkaloids from the Philippine Medicinal Plant Phaeanthus ophthalmicus

Phaeanthus ophthalmicus (Roxb. ex G.Don) J.Sinclair (previously known as P. ebracteolatus (Presl) Merr) is a Philippine medicinal plant occurring as evergreen shrub in the lowland forests of Luzon islands. It is used traditionally by Filipinos to treat bacterial conjunctivitis, ulcer and wound infections. Based on previous investigations where cyclooxygenase-2 (COX-2) functions as immune-linked factor in infectious sensitivities to bacterial pathogens by triggering pro-inflammatory immune-associated reactions, we investigated the antimicrobial and COX inhibitory activities of the extracts and tetrahydrobisbenzylisoquinoline alkaloids of P. ophthalmicus in vitro and in silico to validate its ethnomedicinal uses. Thus, the dichloromethane-methanol (DCM-MeOH) crude extract and alkaloid extracts exhibiting antibacterial activities against drug-resistant bacterial strains such as methicillin-resistance Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus (VRE), Klebsiella pneumoniae + CRE and Pseudomonas aeruginosa + MBL afforded (+)-tetrandrine (1) and (+)-limacusine (2) as the major biologically active tetrahydrobisbenzylisoquinoline alkaloidal constituents after purification. Both tetrahydrobisbenzylisoquinoline alkaloids 1 and 2 showed broad spectrum antibacterial activity with strongest inhibition against the Gram-negative bacteria MβL-Pseudomonas aeruginosa Klebsiella pneumoniae + CRE. Interestingly, the alkaloid limacusine (2) showed selective inhibition against ovine COX-2 in vitro. These results were ascertained by molecular docking and molecular dynamics simulation experiments where alkaloid 2 showed strong affinity in the catalytic sites of Gram-negative bacterial enzymes P. aeruginosa elastase and K. pneumoniae KPC-2 carbapenemase (enzymes involved in infectivity mechanisms), and of ovine COX-2. Overall, our study provides credence on the ethnomedicinal use of the Philippine medicinal plant P. ophthalmicus as traditional plant-based adjuvant to treat bacterial conjunctivitis and other related infections. The antibacterial activities and selective COX-2 inhibition observed for limacusine (2) point to its role as the biologically active constituent of P. ophthalmicus. A limited number of drugs with COX-2 inhibitory properties like celecoxib also confer antibacterial activity. Thus, tetrahydrobisbenzyl alkaloids, especially 2, are promising pharmaceutical inspirations for developing treatments of bacterial/inflammation-related infections.

Evaluation of flavonoids as 2019-nCoV cell entry inhibitor through molecular docking and pharmacological analysis

The outbreak of Coronavirus Disease 2019 (COVID-19) has been declared as a Public Health Emergency of International Concern (PHEIC) by the World Health Organization (WHO), which is being rapidly spread by the extremely spreadable and pathogenic 2019 novel coronavirus (2019-nCoV), also known as SARS-CoV-2. Pandemic incidence of COVID-19 has created a severe threat to global public health, necessitating the development of effective drugs or inhibitors or therapeutics agents against SARS-CoV-2. Spike protein (S) of the SARS-CoV-2 plays a crucial role in entering viruses into the host cell by binding to angiotensin-converting enzyme 2 (ACE-2), and this specific interaction represents a promising drug target for the identification of potential drugs. This study aimed at the receptor-binding domain of S protein (RBD of nCoV-SP) and the ACE-2 receptor as a promising target for developing drugs against SARS-CoV-2. Over 100 different flavonoids with antioxidant, anti-inflammatory, and antiviral properties from different literatures were taken as a ligand or inhibitor for molecular docking against target protein RBD of nCoV-SP and ACE-2 using PyRX and iGEMDOCK. Top flavonoids based on docking scores were selected for the pharmacokinetic study. Selected flavonoids (hesperidin, naringin, ECGC, and quercetin) showed excellent pharmacokinetics with proper absorption, solubility, permeability, distribution, metabolism, minimal toxicity, and excellent bioavailability. Molecular dynamics simulation studies up to 100 ns exhibited strong binding affinity of selected flavonoids to RBD of nCoV-SP and ACE-2, and the protein-ligand complexes were structurally stable. These identified lead flavonoids may act as potential compounds for developing effective drugs against SARS-CoV-2 by potentially inhibiting virus entry into the host cell.

Immunoinformatics and molecular dynamics studies to predict T-cell-specific epitopes of four Klebsiella pneumoniae fimbriae antigens

Klebsiella pneumoniae (K. pneumoniae) is a causative agent of severe infections in humans. There is no publically available vaccine for K. pneumoniae infections yet. Here, using comprehensive immunoinformatics methods, T-cell-specific epitopes of four type 1 fimbriae antigens of K. pneumoniae were predicted and evaluated as potential vaccine candidates. Both CD8+ (class I) and CD4+ (class II) T-cell-specific epitopes were predicted and the epitopes similar to human proteome were excluded. Subsequently, the windows of class-II epitopes containing class-I epitopes were determined. The immunogenicity, IFN-γ production and population coverage were also estimated. Using the 3D structure of HLA and epitopes, molecular docking was carried out. Two best epitopes were selected for molecular dynamics studies. Our prediction and analyses resulted in the several dominant epitopes for each antigen. The docking results showed that all selected epitopes can bind to their restricted HLA molecules with high affinity. The molecular dynamics results indicated the stability of system with minimum possible deviation, suggesting the selected epitopes can be promising candidates for stably binding to HLA molecules. Altogether, our results suggest that the selected T-cell-specific epitopes of K. pneumoniae fimbriae antigens, particularly the two epitopes confirmed by molecular dynamics, can be applied for vaccine development. However, the in vitro and in vivo studies are required to authenticate the results of the present study.Communicated by Ramaswamy H. Sarma.

Identification of potential inhibitors against SARS-CoV-2 by targeting proteins responsible for envelope formation and virion assembly using docking based virtual screening, and pharmacokinetics approaches

WHO has declared the outbreak of COVID-19 as a public health emergency of international concern. The ever-growing new cases have called for an urgent emergency for specific anti-COVID-19 drugs. Three structural proteins (Membrane, Envelope and Nucleocapsid protein) play an essential role in the assembly and formation of the infectious virion particles. Thus, the present study was designed to identify potential drug candidates from the unique collection of 548 anti-viral compounds (natural and synthetic anti-viral), which target SARS-CoV-2 structural proteins. High-end molecular docking analysis was performed to characterize the binding affinity of the selected drugs-the ligand, with the SARS-CoV-2 structural proteins, while high-level Simulation studies analyzed the stability of drug-protein interactions. The present study identified rutin, a bioflavonoid and the antibiotic, doxycycline, as the most potent inhibitor of SARS-CoV-2 envelope protein. Caffeic acid and ferulic acid were found to inhibit SARS-CoV-2 membrane protein while the anti-viral agent's simeprevir and grazoprevir showed a high binding affinity for nucleocapsid protein. All these compounds not only showed excellent pharmacokinetic properties, absorption, metabolism, minimal toxicity and bioavailability but were also remain stabilized at the active site of proteins during the MD simulation. Thus, the identified lead compounds may act as potential molecules for the development of effective drugs against SARS-CoV-2 by inhibiting the envelope formation, virion assembly and viral pathogenesis.

High clinical impact of rapid susceptibility testing on CHROMID ESBL® medium directly from swabs

Background

Antibiotic resistance is a serious public health challenge exacerbated by the widespread use of β-lactam and glycopeptide antibiotics. The identification of resistances is crucial, and CHROMID ESBL medium has been developed to detect enterobacteria with extended-spectrum β-lactamases (ESBL). The objective of this study was to evaluate the potential of this medium to detect other types of resistant bacteria.

Methods

Vancomycin, cefoxitin, imipenem, and cefepime disks were used to measure growth on CHROMID ESBL medium of β-lactam-resistant Gram-negative (83 with ESBL, 57 with carbapenemases, 35 with AmpC and 3 Stenotrophomonas maltophilia) and Gram-positive [37 vancomycin-susceptible (vancoS) microorganisms and 21 vancomycin-resistant (vancoR) Enterococcus faecium] clinical isolates (retrospective study) and colonization by the aforementioned bacteria (prospective study), using 649 rectal swabs, 314 pharyngeal swabs, and 44 swabs from other localizations.

Results

Retrospective study: species grown on the medium exhibited different colors. Growth on the medium was observed for: all ESBL enterobacteria, which were susceptible to imipenem and cefoxitin; 95% of isolates with carbapenemases, mostly resistant to imipenem; 80% of those with AmpC; 86% of vancoR E. faecium isolates; and 42% of vancoS E. faecalis isolates, with large growth inhibition halos around the vancomycin disk. Prospective study: vancoR E. faecium, ESBL Klebsiella, Pseudomonas with carbapenemases, A. baumannii (mostly from rectal swabs), S. maltophilia, Achromobacter xylosoxidans, and Burkholderia cenocepacia (mostly from pharyngeal swabs) were isolated from the 246 positive samples.

Conclusions

CHROMID ESBL medium permitted the differential growth of Gram-negative bacteria, many with ESBL and carbapenemases. ESBL enterobacteria were susceptible to imipenem, carbapenemase-producing microorganisms grew around the imipenem disk, and vancoR E. faecium was isolated on the medium. Results of the prospective study demonstrate the potential clinical relevance of this medium. S. maltophilia was more frequently detected with pharyngeal swabs and ESBL Klebsiella, A. baumannii, and Pseudomonas with rectal swabs.

Computational modeling for mutational analysis of nitrilase enzyme towards enhancement of binding empathy

Nitrilase enzyme (a green catalyst) is an industrially important enzyme which hydrolyses various nitrile compounds (containing -CN functional group) into amides and corresponding carboxylic acids. The current study explored the binding affinity and a method to enhance the catalysis activity of the enzyme using computational approaches. Four mutants were generated using sequential site-directed mutagenesis aiming that an increase in hydrogen bonds that will further increase binding efficiency towards the ligand. Molecular dynamics simulation was rigorously performed to check the stability of those mutants followed by docking to verify its interaction with the ligand. Various statistical dynamics analyses were performed to validate the structure. All the studies predict that built mutants are stable. Mutants 2 and 3 showed a better affinity towards acrylamide by forming the highest number of hydrogen bonds implying better catalysis. The binding affinity values of the Mutant 2 and Mutant 3 with acrylamide are -7.44 kcal/mol and -7.17 kcal/mol, respectively. This study may prove useful for the industry to develop efficient nitrilase enzymes with improved catalytic activity.Communicated by Ramaswamy H. Sarma.

Evaluation of potential drugs against leishmaniasis targeting catalytic subunit of Leishmania donovani nuclear DNA primase using ligand based virtual screening, docking and molecular dynamics approaches

Leishmania donovani, causes leishmaniasis, a global health trouble with around 89 different countries and its population under its risk. Replication initiation events have been instrumental in regulating the DNA duplication and as the small subunit of L. donovani nuclear DNA primase (Ld-PriS) inherits the catalytic site, it plays a vital role in DNA replication. In this study we have aimed Ld-PriS for the first time as a prospective target for the application of drug against Leishmania parasite. 3-D structures of Ld-PriS were built and ligand-based virtual screening was performed using hybrid similarity recognition techniques. Ligands from the ZINC database were used for the screening purposes based on known DNA primase inhibitor Sphingosine as a query. Top 150 ligands were taken into consideration for molecular docking against the query protein (Ld-PriS) using PyRx and iGEMDOCK softwares. Top five compounds with the best docking score were selected for pharmacokinetic investigation and molecular dynamic simulation. These top five screened inhibitors showed very poor binding affinity toward the catalytic subunit of human primase indicating their safety toward the host normal replication mechanism. The top five compounds showed good pharmacokinetic profiles and ADMET predictions revealed good absorption, solubility, permeability, uniform distribution, proper metabolism, minimal toxicity and good bioavailability. Simulation studies upto 50 ns revealed the three leads ZINC000009219046, ZINC000025998119 and ZINC000004677901 bind with Ld-PriS throughout the simulation and there were no huge variations in their backbone suggesting that these three may play as potential lead compounds for developing new drug against leishmaniasis.Communicated by Ramaswamy H. Sarma.

Identification of new DNA gyrase inhibitors based on bioactive compounds from streptomyces: structure-based virtual screening and molecular dynamics simulations approaches

DNA gyrase enzyme has vital role in bacterial survival and can be considered as a potential drug target. Owing to the appearance of resistance to gyrase-targeted drugs, especially fluoroquinolone, screening new compounds which bind more efficiently to the mutant binding pocket is essential. Hence, in this work, using Smina Autodock and through structure-based virtual screening of StreptomeDB, several natural products were discovered based on the SimocyclinoneD8 (SD8) binding pocket of GyrA subunit of DNA gyrase. After evaluation of binding affinity, binding modes, critical interactions and physicochemical and pharmaceutical properties, three lead compounds were selected for further analysis. Afterward 60 ns molecular dynamics simulations were performed and binding free energies were calculated by the molecular mechanics/Poisson-Boltzmann surface area method. Also, interaction of the selected lead compounds with the mutated GyrA protein was evaluated. Results indicated that all of the selected compounds could bind to the both wild-type and mutated GyrA with the binding affinities remarkably higher than SimocyclinoneD8. Interestingly, we noticed that the selected compounds comprised angucycline moiety in their structure which could sufficiently interact with GyrA and block the DNA binding pocket of DNA gyrase, in silico. In conclusion, three DNA gyrase inhibitors were identified successfully which were highly capable of impeding DNA gyrase and can be considered as potential drug candidates for treatment of fluoroquinolone-resistant strains.Communicated by Ramaswamy H. Sarma.