Exploring the molecular interaction of pheniramine with Enterococcus faecalis homoserine kinase: In-silico studies.

Infections caused by the bacteria Enterococcus faecalis (also known as E. faecalis) are common in hospitals. This bacterium is resistant to a wide range of medicines and causes a variety of nosocomial infections. An increase in the number of infections caused by multidrug-resistant (MDR) bacteria is causing substantial economic and health issues around the world. Consequently, new therapeutic techniques to tackle the growing threat of E. faecalis infections must be developed as soon as possible. In this regard, we have targeted a protein that is regarded to be critical for the survival of bacteria in this experiment. Homoserine kinase (HSK) is a threonine metabolism enzyme that belongs to the GHMP kinase superfamily. It is a crucial enzyme in threonine metabolism. This enzyme is responsible for a critical step in the threonine biosynthesis pathway. Given the important function that E. faecalis Homoserine Kinase (ESK) plays in bacterial metabolism, we report here cloning, expression, purification and structural studies of E. faecalis HSK using homology modelling. In addition, we have reported on the model's molecular docking and Molecular Dynamic Stimulation (MD Stimulation) investigations to validate the results of the docking experiments. The results were promising. In silico investigations came up with the conclusion: pheniramine has good binding affinity for the E. faecalis HSK.

Identification of Protein Drug Targets of Biofilm Formation and Quorum Sensing in Multidrug Resistant Enterococcus faecalis.

Enterococcus faecalis (E. faecalis) is an opportunistic multidrug-resistant (MDR) pathogen found in the guts of humans and farmed animals. Due to the occurrence of (MDR) strain there is an urgent need to look for an alternative treatment approach. E. faecalis is a Gram-positive bacterium, which is among the most prevalent multidrug resistant hospital pathogens. Its ability to develop quorum sensing (QS) mediated biofilm formation further exacerbates the pathogenicity and triggers lifethreatening infections. Therefore, developing a suitable remedy for curing E. faecalis mediated enterococcal infections is an arduous task. Several putative virulence factors and proteins are involved in the development of biofilms in E. faecalis. Such proteins often play important roles in virulence, disease, and colonization by pathogens. The elucidation of the structure-function relationship of such protein drug targets and the interacting compounds could provide an attractive paradigm towards developing structure-based drugs against E. faecalis. This review provides a comprehensive overview of the current status, enigmas that warrant further studies, and the prospects toward alleviating the antibiotic resistance in E. faecalis. Specifically, the role of biofilm and quorum sensing (QS) in the emergence of MDR strains had been elaborated along with the importance of the protein drug targets involved in both the processes.

Deciphering the Role of S-adenosyl Homocysteine Nucleosidase in Quorum Sensing Mediated Biofilm Formation.

S-adenosylhomocysteine nucleosidase (MTAN) is a protein that plays a crucial role in several pathways of bacteria that are essential for its survival and pathogenesis. In addition to the role of MTAN in methyl-transfer reactions, methionine biosynthesis, and polyamine synthesis, MTAN is also involved in bacterial quorum sensing (QS). In QS, chemical signaling autoinducer (AI) secreted by bacteria assists cell to cell communication and is regulated in a cell density-dependent manner. They play a significant role in the formation of bacterial biofilm. MTAN plays a major role in the synthesis of these autoinducers. Signaling molecules secreted by bacteria, i.e., AI-1 are recognized as acylated homoserine lactones (AHL) that function as signaling molecules within bacteria. QS enables bacteria to establish physical interactions leading to biofilm formation. The formation of biofilm is a primary reason for the development of multidrug-resistant properties in pathogenic bacteria like Enterococcus faecalis (E. faecalis). In this regard, inhibition of E. faecalis MTAN (EfMTAN) will block the QS and alter the bacterial biofilm formation. In addition to this, it will also block methionine biosynthesis and many other critical metabolic processes. It should also be noted that inhibition of EfMTAN will not have any effect on human beings as this enzyme is not present in humans. This review provides a comprehensive overview of the structural-functional relationship of MTAN. We have also highlighted the current status, enigmas that warrant further studies, and the prospects for identifying potential inhibitors of EfMTAN for the treatment of E. faecalis infections. In addition to this, we have also reported structural studies of EfMTAN using homology modeling and highlighted the putative binding sites of the protein.

Potential Inhibitors of SARS-CoV-2 Main Protease (Mpro) Identified from the Library of FDA-Approved Drugs Using Molecular Docking Studies.

The Corona Virus Infectious Disease-2019 (COVID-19) outbreak originated at Wuhan, China, in December 2019. It has already spread rapidly and caused more than 6.5 million deaths worldwide. Its causal agent is a beta-coronavirus named SARS-CoV-2. Many efforts have already been made to develop new vaccines and drugs against these viruses, but over time, it has changed its molecular nature and evolved into more lethal variants, such as Delta and Omicron. These will lead us to target its more-conserved proteins. The sequences' BLAST and crystal structure of the main protease Mpro suggest a high sequence and structural conservation. Mpro is responsible for the proteolytic maturation of the polyprotein essential for the viral replication and transcription, which makes it an important drug target. Discovery of new drug molecules may take years before getting to the clinics. So, considering urgency, we performed molecular docking studies using FDA-approved drugs to identify molecules that could potentially bind to the substrate-binding site and inhibit SARS-CoV-2's main protease (Mpro). We used the Glide module in the Schrödinger software suite to perform molecular docking studies, followed by MM-GBSA-based energy calculations to score the hit molecules. Molecular docking and manual analysis suggest that several drugs may bind and potentially inhibit Mpro. We also performed molecular simulations studies for selected compounds to evaluate protein-drug interactions. Considering bioavailability, lesser toxicity, and route of administration, some of the top-ranked drugs, including lumefantrine (antimalarial), dipyridamole (coronary vasodilator), dihydroergotamine (used for treating migraine), hexoprenaline (anti asthmatic), riboflavin (vitamin B2), and pantethine (vitamin B5) may be taken forward for further in vitro and in vivo experiments to investigate their therapeutic potential.

In silico prediction, molecular docking and binding studies of acetaminophen and dexamethasone to Enterococcus faecalis diaminopimelate epimerase.

Enterococcus faecalis (E. faecalis) is a Gram-positive coccoid, non-sporulating, facultative anaerobic, multidrug resistance bacterium responsible for almost 65% to 80% of all enterococcal nosocomial infections. It usually causes infective endocarditis, urinary tract and surgical wound infections. The increase in E. faecalis resistance to conventionally available antibiotic has rekindled intense interest in developing useful antibacterial drugs. In E. faecalis, diaminopimelate epimerase (DapF) is involved in the lysine biosynthetic pathway. The product of this pathway is precursors of peptidoglycan synthesis, which is a component of bacterial cell wall. Also, because mammals lack this enzyme, consequently E. faecalis diaminopimelate epimerase (EfDapF) represents a potential target for developing novel class of antibiotics. In this regard, we have successfully cloned, overexpressed the gene encoding DapF in BL-21(DE3) and purified with Ni-NTA Agarose resin. In addition to this, binding studies were performed using fluorescence spectroscopy in order to confirm the bindings of the identified lead compounds (acetaminophen and dexamethasone) with EfDapF. Docking studies revealed that acetaminophen found to make hydrogen bonds with Asn72 and Asn13 while dexamethasone interacted by forming hydrogen bonds with Asn205 and Glu223. Thus, biochemical studies indicated acetaminophen and dexamethasone, as potential inhibitors of EfDapF and eventually can reduce the catalytic activity of EfDapF.

Prevalence and determinants of the dangerous selfie among medical and nursing students: a cross-sectional study from eastern India.

BACKGROUND: Globally, there has been an exponential rise in smartphone use and selfie taking among youth. To make selfies exciting, dangerous selfies are often taken that may lead to catastrophic consequences, including death. This study aims to estimate the prevalence of dangerous selfies and to determine the factors associated with dangerous selfies among medical and nursing students in India. METHODS: The study was conducted at the All India Institute of Medical Sciences (AIIMS), Bhubaneswar, India, in April-August 2018. The inclusion criteria were students enrolled in the Bachelor of Medicine and Bachelor of Surgery (MBBS) and nursing courses of AIIMS, Bhubaneswar. Students who did not use smartphones were excluded from the study. The interview schedule and Selfitis Behaviour Scale (SBS) were used to collect information on sociodemographic variables, smartphone use and variables related to selfies and dangerous selfies. Forward stepwise logistic regression was undertaken with the probability of entry and removal as 0.05 and 0.10, respectively. RESULTS: Of 633 eligible participants, 595 were included in the study. The mean (SD) age of the participants was 21.2 (1.6) years. More than half (56.8%) of the participants were female, 384 (64.5%) were medical students and 211 (35.5%) were nursing students. Nearly two-thirds of the participants (70.6%) preferred to take selfie. One hundred thirty three (40.3%) of the participants posted selfies on social media daily. The prevalence of dangerous selfies was 8.74% (95% CI: 6.73-11.28). Eight injury episodes while taking selfies were reported by seven (1.2%) participants. Being male (AOR 4.96, 95% CI 2.53-9.74), posting selfies on social media daily (AOR 3.33, 95% CI 1.71-6.47) and an SBS score > 75 (AOR 4.97, 95% CI 1.43-17.28) were independent predictors of dangerous selfies. CONCLUSION: Nearly one in ten medical and nursing students reported having taken a dangerous selfie, and one in one hundred reported having been injured while attempting to take a selfie. Being male, posting selfies on social media daily and an SBS score > 75 were independent predictors of dangerous selfies. Further research is required to identify the community burden of dangerous selfies and to develop strategies to prevent selfie-related fatalities among youths.

Prospecting Potential Inhibitors of Sortase A from Enterococcus faecalis: A Multidrug Resistant Bacteria, through In-silico and In-vitro Approaches.

BACKGROUND: Enterococcus faecalis (Ef) infections are becoming dreadfully common in hospital environments. Infections caused by Ef are difficult to treat because of its acquired resistance to different class of antibiotics, making it a multidrug resistant bacteria. Key pathogenic factor of Ef includes its ability to form biofilm on the surface of diagnostic and other medical devices. Sortase A (SrtA) is a cysteine transpeptidase which plays a pivotal role in the formation of biofilm in Ef, hence, it is considered as an important enzyme for the pathogenesis of Ef. Thus, inhibition of (SrtA) will affect biofilm formation, which will reduce its virulence and eventually Ef infection will be abridged. OBJECTIVE: To find potential inhibitors of Enterococcus faecalis Sortase A (EfSrtA) through insilico and in-vitro methods. METHODS: Gene coding for EfSrtA was cloned, expressed and purified. Three-dimensional model of EfSrtA was created using Swiss-Model workspace. In-silico docking studies using Autodock vina and molecular dynamics simulations of the modelled structures using Gromacs platform were performed to explore potential lead compounds against EfSrtA. In-vitro binding experiments using spectrofluorometric technique was carried out to confirm and validate the study. RESULTS: In-silico docking and in-vitro binding experiments revealed that curcumin, berberine and myricetin bound to EfSrtA at nanomolar concentrations with high affinity. CONCLUSION: This is a first structural report of EfSrtA with curcumin, berberine and myricetin. Taking in account the herbal nature of these compounds, the use of these compounds as inhibitors will be advantageous. This study validated curcumin, berberine and myricetin as potential inhibitors of EfSrtA.

In search of novel protein drug targets for treatment of Enterococcus faecalis infections.

Enterococcus faecalis (Ef) is one of the major pathogens involved in hospital-acquired infections. It can cause nosocomial bacteremia, surgical wound infection, and urinary tract infection. It is important to mention here that Ef is developing resistance against many commonly occurring antibiotics. The occurrence of multidrug resistance (MDR) and extensive-drug resistance (XDR) is now posing a major challenge to the medical community. In this regard, to combat the infections caused by Ef, we have to look for an alternative. Rational structure-based drug design exploits the three-dimensional structure of the target protein, which can be unraveled by various techniques such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. In this review, we have discussed the complete picture of Ef infections, the possible treatment available at present, and the alternative treatment options to be explored. This study will help in better understanding of novel biological targets against Ef and the compounds, which are likely to bind with these targets. Using these detailed structural informations, rational structure-based drug design is achievable and tight inhibitors against Ef can be prepared.

Identification and evaluation of quercetin as a potential inhibitor of naphthoate synthase from Enterococcus faecalis.

Enterococcus faecalis is a gram-positive, rod-shape bacteria responsible for around 65% to 80% of all enterococcal nosocomial infections. It is multidrug resistant (MDR) bacterium resistant to most of the first-line antibiotics. Due to the emergence of MDR strains, there is an urgent need to find novel targets to develop new antibacterial drugs against E. faecalis. In this regard, we have identified naphthoate synthase (1,4-dihydroxy-2-naphthoyl-CoA synthase, EC: 4.1.3.36; DHNS) as an anti-E. faecalis target, as it is an essential enzyme for menaquinone (vitamin K2 ) synthetic pathway in the bacterium. Thus, inhibiting naphtholate synthase may consequently inhibit the bacteria's growth. In this regard, we report here cloning, expression, purification, and preliminary structural studies of naphthoate synthase along with in silico modeling, molecular dynamic simulation of the model and docking studies of naphthoate synthase with quercetin, a plant alkaloid. Biochemical studies have indicated quercetin, a plant flavonoid as the potential lead compound to inhibit catalytic activity of EfDHNS. Quercetin binding has also been validated by spectrofluorimetric studies in order to confirm the bindings of the ligand compound with EfDHNS at ultralow concentrations. Reported studies may provide a base for structure-based drug development of antimicrobial compounds against E. faecalis.

Identification of potential inhibitors of sortase A: Binding studies, in-silico docking and protein-protein interaction studies of sortase A from Enterococcus faecalis.

Enterococcus faecalis (Ef) is a Gram positive multidrug resistant (MDR) bacterium contributing about 70% of total enterococcal infections. In Ef, a membrane anchored transpeptidase Sortase A plays a major role in biofilm formation. Therefore, it has been recognized as an ideal drug target against Ef. In this regard to identify the potential inhibitors of Ef Sortase A (EfSrtA∆59), we have cloned, expressed and purified EfSrtA∆59. We have also done the in-silico docking studies to identify lead molecules interacting with EfSrtA∆59. Furthermore, the binding studies of these identified lead molecules were performed with EfSrtA∆59 using fluorescence and CD spectroscopic studies. We also identified the interaction partner of EfSrtA∆59 using STRING. Protein-protein docking studies were also performed. Docking experiment revealed that benzylpenicillin, cefotaxime, pantoprazole and valsartan were bound to same site on the protein with similar interactions. Binding studies using fluorescence spectroscopic studies confirmed the binding of all the ligands to EfSrtA∆59, which was further validated by far and near-UV CD experiments. Thermo stability experiments validate the stability-activity trade-off hypothesis. Sequence based interaction studies identified that EfSrtA∆59 interact with the Ef_1091, Ef_1093 and Ef_2658 proteins. Homology model of Ef_1091 and Ef_1093 was docked with modeled EfSrtA∆59 and their interactions are also discussed.

Antibacterial Synergy of Silver Nanoparticles with Gentamicin and Chloramphenicol against Enterococcus faecalis.

BACKGROUND: Enterococcus faecalis (Ef) is a multidrug-resistant pathogenic bacteria associated with hospital-acquired infections. Ef is involved in a number of infectious diseases. It generally infects patients with the weekend immune system, i.e. a person mostly acquires Ef infections in the hospital, especially in intensive care units and thus, is more likely to be resistant to many antibiotics. Development of resistance against various antibiotics and emergence of drug-resistant strains is a growing global concern. OBJECTIVE: Due to the unselective use of antibiotics for a long time multidrug resistant bacteria and extensively drug-resistant, which is now posing a new challenge to the medical community. To treat infections caused by Ef, the synergistic effect of different antibiotics with silver nanoparticles (AgNPs) was tested against Ef. MATERIALS AND METHODS: In the present study, synthesis of AgNPs was carried out from the cell-free supernatant of Klebsiella pneumoniae. AgNPs were characterized using various techniques, namely, ultraviolet-visible spectrophotometry, transmission electron microscopy, and Fourier transform infrared spectroscopy. Moreover, process optimization was done for enhanced production of AgNPs. In addition, antimicrobial activity of the nanoparticles was also tested. Furthermore, the nanoparticles were evaluated for their antimicrobial activities in combination with gentamicin and chloramphenicol, against Ef. RESULTS: The results showed that the combination of gentamicin and chloramphenicol with AgNPs has a better antibacterial effect. To add to this, hemolytic activity of AgNPs was evaluated against human red blood corpuscles (RBCs). AgNPs were found to be nontoxic to RBCs. CONCLUSION: The collective effect of AgNps with Gentamicin and Chloramphenicol was more as compared to AgNps alone which indicate the synergistic effect of these components. These observations show the potential of AgNPs in combination with above-stated antibiotics against Ef infections. SUMMARY: Enterococcus faecalis (Ef) is a multidrug-resistant bacteria with is resistant to wide range of antibioticsDue to this increasing resistance, there is a need to find a new approach to overcome the infections caused by EfThe combined effect of silver nanoparticles (AgNPs) with gentamicin and chloramphenicol was notably seen against EfFurthermore, the AgNPs were nontoxic to the human red blood corpuscles which confirm its nontoxic nature. Abbreviations used: Ef: Enterococcus faecalis, MDR: Multidrug resistance, AgNPs: Silver nanoparticles, Kp: Klebsiella pneumoniae, RBCs: Red blood corpuscles, ENPs: Engineered nanoparticles, FTIR: Fourier transform infrared spectroscopy, TEM: Transmission electron microscopy, AgNO3: Silver nitrate, EDTA: Ethylenediaminetetraacetic acid, PBS: Phosphate-buffered saline.