In silico validation of the non-antibiotic drugs acetaminophen and ibuprofen as antibacterial agents against red complex pathogens

Databases of ligand-binding pockets and protein-ligand interactions

Many research groups and institutions have created a variety of databases curating experimental and predicted data related to protein-ligand binding. The landscape of available databases is dynamic, with new databases emerging and established databases becoming defunct. Here, we review the current state of databases that contain binding pockets and protein-ligand binding interactions. We have compiled a list of such databases, fifty-three of which are currently available for use. We discuss variation in how binding pockets are defined and summarize pocket-finding methods. We organize the fifty-three databases into subgroups based on goals and contents, and describe standard use cases. We also illustrate that pockets within the same protein are characterized differently across different databases. Finally, we assess critical issues of sustainability, accessibility and redundancy.

Computational Modelling, Functional Characterization and Molecular Docking to Lead Compounds of Bordetella pertussis Diaminopimelate Epimerase

Bordetella pertussis, the causative agent of whooping cough, is an opportunistic virulent bacterial pathogen that is resistant to a wide range of antibiotics due to a variety of resistance mechanisms. Looking at the increasing number of infections caused by B. pertussis and its resistance to diverse antibiotics, it is essential to develop alternative strategies to fight against B. pertussis. Diaminopimelate epimerase (DapF) is an important enzyme of the lysine biosynthesis pathway in B. pertussis that catalyzes the formation of meso-2, 6-diaminoheptanedioate (meso-DAP), which is an important step in lysine metabolism. Therefore, Bordetella pertussis diaminopimelate epimerase (DapF) becomes an ideal target for antimicrobial drug development. In the present study, computational modelling, functional characterization, binding studies, and docking studies of BpDapF with lead compounds were carried out using different in silico tools. In silico prediction results in the secondary structure, 3-D structure analysis, and protein-protein interaction analysis of BpDapF. Docking studies further showed the respective amino acid residues for ligands in the phosphate‑binding loop of BpDapF play a vital role in the formation of H‑bonds with these ligands. The site where the ligand was bound is a deep groove, which is regarded as the binding cavity of the protein. Biochemical studies indicated that Limonin (binding energy - 8.8 kcal/mol), Ajmalicine (binding energy - 8.7 kcal/mol), Clinafloxacin (binding energy - 8.3 kcal/mol), Dexamethasone (binding energy - 8.2 kcal/mol), and Tetracycline (binding energy - 8.1 kcal/mol) exhibited promising binding towards the drug target DapF of B. pertussis in comparison with the binding between other drugs and act as the potential inhibitors of BpDapF that eventually can reduce the catalytic activity of BpDapF.

Antimicrobial and antibiofilm activity of fungal metabolites on methicillin-resistant Staphylococcus aureus (ATCC 43300) mediated by SarA and AgrA

Methicillin-resistant Staphylococcus aureus (MRSA) increases its antibiotic resistance by forming biofilms. Natural products (NP) or specialized metabolites have demonstrated their ability to decrease the virulence and pathogenesis of MRSA infections by inhibiting biofilm formation. The present study evaluated the antimicrobial and antibiofilm potential against MRSA of a small library of fungal NP isolated from Mexican biodiversity. The most potent antibacterial activity was observed for myrotecisin B, epiequisetin, equisetin, stachybotrolide acetate, monorden A, zearalenone, fuscin, and fusarubin. On the other hand, epifiscalin C, fiscalin C, dimethylglyotoxin, aspernolide B, and butyrolactones I and IV inhibited the biofilm formation without decreasing bacterial growth. To determine the putative mechanism of action of these compounds, docking analyses were performed against SarA and AgrA proteins, targets known to regulate biofilm production in MRSA. Overall, the results demonstrate that fungal NP may act as potential antibiofilm agents for treating MRSA infections.

Drug repurposing to overcome microbial resistance

Infections are a growing global threat, and the number of resistant species of microbial pathogens is alarming. However, the rapid development of cross-resistant or multidrug-resistant strains and the development of so-called 'superbugs' are in stark contrast to the number of newly launched anti-infectives on the market. In this review, I summarize the causes of antimicrobial resistance, briefly discuss different approaches to the discovery and development of new anti-infective drugs, and focus on drug repurposing strategy, which is discussed from all possible perspectives. A comprehensive overview of drugs of other indications tested for their in vitro antimicrobial activity to support existing anti-infective therapeutics is provided, including several critical remarks on this strategy of repurposing non-antibiotics to antibacterial drugs.

Multidrug resistance crisis during COVID-19 pandemic: Role of anti-microbial peptides as next-generation therapeutics

The decreasing effectiveness of conventional drugs due to multidrug-resistance is a major challenge for the scientific community, necessitating development of novel antimicrobial agents. In the present era of coronavirus 2 (COVID-19) pandemic, patients are being widely exposed to antimicrobial drugs and hence the problem of multidrug-resistance shall be aggravated in the days to come. Consequently, revisiting the phenomena of multidrug resistance leading to formulation of effective antimicrobial agents is the need of the hour. As a result, this review sheds light on the looming crisis of multidrug resistance in wake of the COVID-19 pandemic. It highlights the problem, significance and approaches for tackling microbial resistance with special emphasis on anti-microbial peptides as next-generation therapeutics against multidrug resistance associated diseases. Antimicrobial peptides exhibit exceptional mechanism of action enabling rapid killing of microbes at low concentration, antibiofilm activity, immunomodulatory properties along with a low tendency for resistance development providing them an edge over conventional antibiotics. The review is unique as it discusses the mode of action, pharmacodynamic properties and application of antimicrobial peptides in areas ranging from therapeutics to agriculture.

Identification of docosahexaenoic and eicosapentaenoic acids multiple targets facing periodontopathogens

The eicosapentaenoic (EPA) and docosahexaenoic acid (DHA) play a substantial role in Periodontal Disease (PD) due to their antimicrobial and immunomodulatory actions. However, their antimicrobial mechanism of action against bacteria involved in PD remains unclear. We aimed to estimate the probable targets of EPA and DHA against the seven periodontopathogens. Through in silico analyses, the protein-acids interactions, protein characterization, and molecular docking were performed. We identified 165 proteins from periodontopathogens that may interact with EPA and DHA. Fusobacterium nucleatum has the highest number of predicted proteins among analyzed bacteria (n = 43, 26.06%). The EPA shows more interactions than DHA. The EPA and DHA interact mainly with proteins involved in the metabolism (n = 69, 41.81%). Also, the EPA and DHA interact with proteins located in any subcellular location. The affinities between acids and pathogenic proteins were moderate (binding energy was lower than -4.0 kcal/mol). The interactions between EPA and DHA and periodontopathogens occur in multiples proteins. There is not a predilection about the functional class of pathogenic proteins targeting EPA and DHA. However, there are moderate binding affinities between EPA or DHA and essential pathogenic proteins (TolC, CRISPR, FusA).

Removal of Ibuprofen at Low Concentration Using a Newly Formulated Emulsion Liquid Membrane

Ibuprofen (IBP) is a pharmaceutical product that is widely prescribed as an over-the-counter painkiller. It has been classified as a contaminant of emerging concern (CEC) that has received global attention in the search for a better wastewater separation technology. The emulsion liquid membrane (ELM) is one of the potential solutions for IBP removal from wastewater owing to its advantages, such as the ability to remove a highly soluble solute, energy efficient and tuneable formulation. To develop this ELM, a series of parameters such as stirring speed, emulsification time, organic to internal phase volume ratio (O/I), internal phase concentration, carrier concentration and surfactant concentration were studied. The extraction was carried out for 15 min stirring time and the concentration of IBP in the feed phase was determined using a UV-Vis spectrophotometer. The optimum formulation for the ELM was found at 300 rpm stirring speed, 20 min emulsification time, 3:1 of O/I, 0.1 M ammonia, NH₃ (stripping agent), 6 wt% trioctylamine, TOA (carrier) and 2 wt% sorbitan monooleate, Span 80 (non-ionic surfactant). IBP removal of 89% was achieved at the optimum parameters of ELM. The current research demonstrated that a newly formulated ELM has great potential in removing a low concentration IBP from wastewater.

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.

Identification of aspirin and diclofenac binding proteins in the red complex pathogens

Red complex organisms are a group of organisms (Porphyromonas gingivalis ATCC 33277, Treponema denticola ATCC 35405, Tannerella forsythia ATCC 43037) that have been identified for the causation of periodontal diseases. Aspirin and diclofenac have been used as regular analgesics. Therefore, it is of interest to document the identification of aspirin and diclofenac binding proteins in the red complex pathogens using the STITCH v.5 pipeline. The virulence properties of these proteins were analyzed using VICMPred and VirulentPred software. Thus, we document 000 number of proteins having optimal binding features with the known analgesics.

Strategies to Combat Multidrug-Resistant and Persistent Infectious Diseases

Antibiotic failure is one of the most worrying health problems worldwide. We are currently facing an international crisis with several problematic facets: new antibiotics are no longer being discovered, resistance mechanisms are occurring in almost all clinical isolates of bacteria, and recurrent infections caused by persistent bacteria are hampering the successful treatment of infections. In this context, new anti-infectious strategies against multidrug-resistant (MDR) and persistent bacteria, as well as the rescue of Food and Drug Administration (FDA)-approved compounds (drug repurposing), are being explored. Among the highlighted new anti-infectious strategies, in this review, we focus on antimicrobial peptides, anti-virulence compounds, phage therapy, and new molecules. As drugs that are being repurposed, we highlight anti-inflammatory compounds, anti-psychotics, anti-helminthics, anti-cancerous drugs, and statins.

Red complex: Polymicrobial conglomerate in oral flora: A review

Oral diseases are the complex host responses composed of a broad array of inflammatory cells, and cytokines, chemokines, and mediators derived from the cells resident in the gingival tissues, as well as from the emigrating inflammatory cells. A chronic polymicrobial challenge to the local host tissues triggers this response, which under certain circumstances, and in a subset of the population, leads to the progressing soft and hard tissue destruction that characterizes periodontitis. The red complex has been proposed as a pathogenic consortium, consisting of P. gingivalis, T. denticola, and T. forsythia. This review has attempted to examine the virulence potential and determinants of these commensal opportunists.