Dihydrofolate reductase inhibitors as antibacterial agents

In-silico evaluation of Bismurrayaquinone-A phytochemical as a potential multifunctional inhibitor targeting dihydrofolate reductase: implications for anticancer and antibacterial drug development

Dihydrofolate reductase (DHFR) has gained significant attention in drug development, primarily due to marked distinctions in its active site among different species. DHFR plays a crucial role in both DNA and amino acid metabolism by facilitating the transfer of monocarbon residues through tetrahydrofolate, which is vital for nucleotide and amino acid synthesis. This considers its potential as a promising target for therapeutic interventions. In this study, our focus was on conducting a virtual screening of phytoconstituents from the IMPPAT2.0 database to identify potential inhibitors of DHFR. The initial criterion involved assessing the binding energy of molecules against DHFR and we screened top 20 compounds ranging energy -13.5 to -11.4 (kcal/Mol) while Pemetrexed disodium bound with less energy -10.2 (kcal/Mol), followed by an analysis of their interactions to identify more effective hits. We prioritized IMPHY007679 (Bismurrayaquinone-A), which displayed a high binding affinity and crucial interaction with DHFR. We also evaluated the drug-like properties and biological activity of IMPHY007679. Furthermore, MD simulation was done, RMSD, RMSF, Rg, SASA, PCA and FEL explore the time-evolution impact of IMPHY007679 comparing it with a reference drug, Pemetrexed disodium. Collectively, our findings suggest that IMPHY007679 recommend further investigation in both in vitro and in vivo settings for its potential in developing anticancer and antibacterial therapies. This compound holds promise as a valuable candidate for advancing drug research and treatment strategies.

Discovery of a Pseudomonas aeruginosa-specific small molecule targeting outer membrane protein OprH-LPS interaction by a multiplexed screen

The surge of antimicrobial resistance threatens efficacy of current antibiotics, particularly against Pseudomonas aeruginosa, a highly resistant gram-negative pathogen. The asymmetric outer membrane (OM) of P. aeruginosa combined with its array of efflux pumps provide a barrier to xenobiotic accumulation, thus making antibiotic discovery challenging. We adapted PROSPECT, a target-based, whole-cell screening strategy, to discover small molecule probes that kill P. aeruginosa mutants depleted for essential proteins localized at the OM. We identified BRD1401, a small molecule that has specific activity against a P. aeruginosa mutant depleted for the essential lipoprotein, OprL. Genetic and chemical biological studies identified that BRD1401 acts by targeting the OM β-barrel protein OprH to disrupt its interaction with LPS and increase membrane fluidity. Studies with BRD1401 also revealed an interaction between OprL and OprH, directly linking the OM with peptidoglycan. Thus, a whole-cell, multiplexed screen can identify species-specific chemical probes to reveal pathogen biology.

Resistance of Wolbachia to Trimethoprim: Insights into Genes Encoding Dihydrofolate Reductase, Thymidylate Synthase and Serine Hydroxymethyltransferase in the Rickettsiales

Bacterial and eukaryotic dihydrofolate reductase (DHFR) enzymes are essential for DNA synthesis and are differentially sensitive to the competitive inhibitors trimethoprim and methotrexate. Unexpectedly, trimethoprim did not reduce Wolbachia abundance, and the wStri DHFR homolog contained amino acid substitutions associated with trimethoprim resistance in E. coli. A phylogenetic tree showed good association of DHFR protein sequences with supergroup A and B assignments. In contrast, DHFR is not encoded by wFol (supergroup E) and wBm (supergroup D) or by genomes of the closely related genera Anaplasma, Ehrlichia, Neorickettsia, and possibly Orientia. In E. coli and humans, DHFR participates in a coupled reactions with the conventional thymidylate synthase (TS) encoded by thyA to produce the dTMP required for DNA synthesis. In contrast, Wolbachia and other Rickettsiales express the unconventional FAD-TS enzyme encoded by thyX, even when folA is present. The exclusive use of FAD-TS suggests that Wolbachia DHFR provides a supplementary rather than an essential function for de novo synthesis of dTMP, possibly reflecting the relative availability of, and competing demands for, FAD and NAD coenzymes in the diverse intracellular environments of its hosts. Whether encoded by thyA or thyX, TS produces dTMP by transferring a methyl group from methylene tetrahydrofolate to dUMP. In the Rickettsiales, serine hydroxymethyltransferase (SMHT), encoded by a conserved glyA gene, regenerates methylene tetrahydrofolate. Unlike thyA, thyX lacks a human counterpart and thus provides a potential target for the treatment of infections caused by pathogenic members of the Rickettsiales.

Molecular modeling, synthesis and biological evaluation of caffeic acid based Dihydrofolate reductase inhibitors

Dihydrofolate reductase (DHFR) is an enzyme that plays a crucial role in folate metabolism, which is essential for cell growth and division. DHFR has been identified as a molecular target for numerous diseases due to its significance in various biological processes. DHFR inhibitors can disrupt folate metabolism by inhibiting DHFR, leading to the inhibition of cell growth. So, a series of caffeic acid derivatives were designed, synthesized, characterized and evaluated for their in vitro ability to inhibit DHFR, as well as their antimicrobial and anticancer properties. Among all synthesized compounds, compound CE11 exhibited the highest DHFR inhibitory activity, with an IC50 value of 0.048 µM, which is approximately four times more potent than methotrexate. Compound CE11 exhibited similar docking performance to methotrexate, binding to the same site and engaging key residues such as Glh30, Phe31, Phe34, and Ser59. It also fit snugly in the hydrophobic pocket of modeled protein. Moreover, substantial hydrophobic interactions were noted between the ligand and the hydrophobic amino acid residues of DHFR. This effectively secured the derivative within the restricted substrate cavity. Furthermore, compound CE11 demonstrated a significant anticancer activity against MCF-7 breast cancer cell line, with an IC50 value of 5.37 ± 0.16 µM. Compounds CE3 and CE15 displayed better antibacterial activity compared to trimethoprim and comparable to ampicillin against the gram-positive bacteria S. aureus. Moreover, compounds CE3 and CE15 have shown better antibacterial activity than standard trimethoprim, ampicillin and tetracycline against the gram-negative bacteria, particularly P. aeruginosa and E. coli. Molecular docking analysis of CE3 revealed that it firmly entrapped into the active site of enzyme through hydrophobic interaction with hydrophobic residues. Additionally, it forms hydrogen bonds with important amino acid residues Ala7, Asn18, and Thr121 with excellent docking score and binding energy (-9.9, -71.77 kcal/mol). These interactions might be contributed to the significant DHFR inhibition and antimicrobial activity. The generated model holds potential value in facilitating the development of a novel category of DHFR inhibitors as anticancer and antimicrobial agents.

Design, Synthesis, Antimicrobial Activity, and Molecular Docking of Novel Thiazoles, Pyrazoles, 1,3-Thiazepinones, and 1,2,4-Triazolopyrimidines Derived from Quinoline-Pyrido[2,3-d] Pyrimidinones

BACKGROUND

Recently, pyrido[2,3-d] pyrimidine, triazolopyrimidine, thiazolopyrimidine, quinoline, and pyrazole derivatives have gained attention due to their diverse biological activities, including antimicrobial, antioxidant, antitubercular, antitumor, anti-inflammatory, and antiviral effects.

OBJECTIVE

The synthesis of new heterocyclic compounds including 5-quinoline-pyrido[2,3-d] pyrimidinone (1-2, 4, 6-7), 6-quinoline-pyrido[2,3-d]thiazolo[3,2-a]pyrimidinone (3, 5, 8-10), 1,2,4-triazole-6-quinoline-pyrido[2,3-d]thiazolo[3,2-a]pyrimidinone (11-13), and pyrido[2,3-d]thiazolo[3,2-a]pyrimidine-ethyl-(pyridine)-9-thiaazabenzo[cd]azulenone (14) derivatives was performed with high yields while evaluating antimicrobial activities.

METHODS

A new series of quinoline-pyrido[2,3-d]thiazolo[3,2-a]pyrimidine derivatives were prepared using a modern style and advanced technology, resulting in high yields of these new compounds. Various reagents were utilized, specifically tailored to the production needs of each compound, through reactions that included alkylation, addition, condensation, acylation, the formation of Schiff bases, and intramolecular cyclization.

RESULTS

The chemical structures of the new compounds were determined using spectroscopy analyses, including IR, NMR, and MS, achieving good yields ranging from 68% to 90% under mild conditions in a regular system. All compounds were tested for in vitro antimicrobial activity and compared to standard drugs, specifically cefotaxime sodium and nystatin. The results showed that compounds 10 to 14 exhibited excellent antimicrobial activity, with a minimum inhibitory concentration (MIC) of 1 to 5 µmol/mL, compared to that of the standard drugs, which had MIC values of 1 to 3 µmol/mL. Furthermore, molecular docking studies were conducted to explore the interactions of specific compounds with antimicrobial target proteins. The findings revealed that compounds 10 to 14 displayed significant binding energies, with ΔG values ranging from -7.20 to -11.70 kcal/mol, indicating effective binding to the active sites of antimicrobial protein receptors.

CONCLUSIONS

The SAR study confirmed a relationship between antimicrobial activity and the tested compounds. Molecular docking demonstrated that compounds 10, 11, 12, 13, and 14 exhibited significant binding energy, effectively interacting with the active sites of antimicrobial protein receptors. This consistent finding supports that these new compounds' practical and theoretical studies align regarding their antimicrobial activity.

Biochemical and biological studies of irradiated and non-irradiated extracts of Solanum aculeastrum Dunal fruit

This study explores the impact of γ-irradiation on ethanolic extracts of Solanum aculeastrum Dunal. The anti-cancer and antimicrobial properties were investigated. The obtained results revealed that total phenol (TP) and total flavonoid (TF) of total ethanol extract (100%) (FTE) were higher than 70% ethanol extract (SE), and these contents increased after gamma radiation with 5 kGy. The results of minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of the Solanum aculeastrum extracts suggested that FTE and 5 kGy-irradiated FTE can be used to control and prevent skin infections caused by MRSA and endocarditis, urinary tract infections, and prostatitis caused by Enterococcus faecalis. The FTE sample irradiated at 5 kGy showed cytotoxicity for A431 and Hct-116 cell lines similar to the control sample and higher than the toxicity revealed by the samples irradiated at 10 kGy. In normal cells (Bj-1), the toxicity was decreased after irradiation (IC50 = 31 μg/ml) compared to the non-irradiated extract (IC50 = 26.1 μg/ml). Molecular docking suggested Sortase A to play a role in chlorogenic acid antibacterial activity towards Staphylococcus aureus. In conclusion, γ-irradiation can be used to enhance the phytoconstituents of Solanum aculeastrum fruit extracts and, consequently, its biological properties.

Design, synthesis, in vitro and in silico studies of novel piperidine derived thiosemicarbazones as inhibitors of dihydrofolate reductase

Dihydrofolate reductase (DHFR), an essential enzyme in folate metabolism, presents a promising target for drug development against various diseases, including cancer and tuberculosis. Herein, we present an integrated approach combining in vitro biochemical assays with in silico molecular docking analysis to evaluate the inhibitory potential of 4-piperidine-based thiosemicarbazones 5(a-s) against DHFR. In our in vitro study, a novel series of 4-piperidine-based thiosemicarbazones 5(a-s) were assessed for their inhibitory activity against DHFR enzyme. The synthesized compounds 5(a-s) exhibited potent inhibition with IC50 values in the range of 13.70 ± 0.25 µM to 47.30 ± 0.86 µM. Among all the derivatives 5p displayed highest inhibitory activity. Simultaneously, in silico analysis were performed and compared with standard drug (Methotrexate) to predict the binding affinity and interaction pattern of synthesized compounds with DHFR active site. SAR analysis was done to elucidate how structural modifications impact compound's biological activity, guiding the rational design of potent and selective drug candidates for targeted diseases. These findings may provide a comprehensive assessment of 4-piperdine-based thiosemicarbazones as DHFR inhibitors and contribute to the development of novel therapeutics targeting DHFR-associated diseases.

Respiratory tract infections: an update on the complexity of bacterial diversity, therapeutic interventions and breakthroughs

Respiratory tract infections (RTIs) have a significant impact on global health, especially among children and the elderly. The key bacterial pathogens Streptococcus pneumoniae, Haemophilus influenzae, Klebsiella pneumoniae, Staphylococcus aureus and non-fermenting Gram Negative bacteria such as Acinetobacter baumannii and Pseudomonas aeruginosa are most commonly associated with RTIs. These bacterial pathogens have evolved a diverse array of resistance mechanisms through horizontal gene transfer, often mediated by mobile genetic elements and environmental acquisition. Treatment failures are primarily due to antimicrobial resistance and inadequate bacterial engagement, which necessitates the development of alternative treatment strategies. To overcome this, our review mainly focuses on different virulence mechanisms and their resulting pathogenicity, highlighting different therapeutic interventions to combat resistance. To prevent the antimicrobial resistance crisis, we also focused on leveraging the application of artificial intelligence and machine learning to manage RTIs. Integrative approaches combining mechanistic insights are crucial for addressing the global challenge of antimicrobial resistance in respiratory infections.

Bacillus subtilis stress-associated mutagenesis and developmental DNA repair

SUMMARYThe metabolic conditions that prevail during bacterial growth have evolved with the faithful operation of repair systems that recognize and eliminate DNA lesions caused by intracellular and exogenous agents. This idea is supported by the low rate of spontaneous mutations (10-9) that occur in replicating cells, maintaining genome integrity. In contrast, when growth and/or replication cease, bacteria frequently process DNA lesions in an error-prone manner. DNA repairs provide cells with the tools needed for maintaining homeostasis during stressful conditions and depend on the developmental context in which repair events occur. Thus, different physiological scenarios can be anticipated. In nutritionally stressed bacteria, different components of the base excision repair pathway may process damaged DNA in an error-prone approach, promoting genetic variability. Interestingly, suppressing the mismatch repair machinery and activating specific DNA glycosylases promote stationary-phase mutations. Current evidence also suggests that in resting cells, coupling repair processes to actively transcribed genes may promote multiple genetic transactions that are advantageous for stressed cells. DNA repair during sporulation is of interest as a model to understand how transcriptional processes influence the formation of mutations in conditions where replication is halted. Current reports indicate that transcriptional coupling repair-dependent and -independent processes operate in differentiating cells to process spontaneous and induced DNA damage and that error-prone synthesis of DNA is involved in these events. These and other noncanonical ways of DNA repair that contribute to mutagenesis, survival, and evolution are reviewed in this manuscript.

Construction and Docking Studies of Novel Pyrimido[4,5-b]quinolines as Antimicrobial Agents

In order to develop novel antimicrobial agents, we prepared quinoline bearing pyrimidine analogues 2-7, 8 a-d and 9 a-d and their structures were elucidated by spectroscopic techniques. Furthermore, our second aim was to predict the interactions between the active compounds and enzymes (DNA gyrase and DHFR). In this work, fourteen pyrimido[4,5-b]quinoline derivatives were prepared and assessed for their antimicrobial potential by estimating zone of inhibition. All the screened candidates displayed antibacterial potential with zone of inhibition range of 9-24 mm compared with ampicillin (20-25 mm) as a reference drug. Moreover, the target derivatives 2 (ZI=16), 9 c (ZI=17 mm) and 9 d (ZI=16 mm) recorded higher antifungal activity against C. albicans to that exhibited by the antifungal drug amphotericin B (ZI=15 mm). Finally, the most potent pyrimidoquinoline compounds (2, 3, 8 c, 8 d, 9 c and 9 d) were docked inside DHFR and DNA gyrase active sites and they recorded excellent fitting within the active regions of DNA gyrase and DHFR. These outcomes revealed us that compounds (2, 3, 8 c, 8 d, 9 c and 9 d) could be lead compounds to discover novel antibacterial candidates.

Designing Antitrypanosomal and Antileishmanial BODIPY Derivatives: A Computational and In Vitro Assessment

Leishmaniasis and Human African trypanosomiasis pose significant public health threats in resource-limited regions, accentuated by the drawbacks of the current antiprotozoal treatments and the lack of approved vaccines. Considering the demand for novel therapeutic drugs, a series of BODIPY derivatives with several functionalizations at the meso, 2 and/or 6 positions of the core were synthesized and characterized. The in vitro activity against Trypanosoma brucei and Leishmania major parasites was carried out alongside a human healthy cell line (MRC-5) to establish selectivity indices (SIs). Notably, the meso-substituted BODIPY, with 1-dimethylaminonaphthalene (1b) and anthracene moiety (1c), were the most active against L. major, displaying IC50 = 4.84 and 5.41 μM, with a 16 and 18-fold selectivity over MRC-5 cells, respectively. In contrast, the mono-formylated analogues 2b and 2c exhibited the highest toxicity (IC50 = 2.84 and 6.17 μM, respectively) and selectivity (SI = 24 and 11, respectively) against T. brucei. Further insights on the activity of these compounds were gathered from molecular docking studies. The results suggest that these BODIPYs act as competitive inhibitors targeting the NADPH/NADP+ linkage site of the pteridine reductase (PR) enzyme. Additionally, these findings unveil a range of quasi-degenerate binding complexes formed between the PRs and the investigated BODIPY derivatives. These results suggest a potential correlation between the anti-parasitic activity and the presence of multiple configurations that block the same site of the enzyme.

"Multiplexed screen identifies a Pseudomonas aeruginosa -specific small molecule targeting the outer membrane protein OprH and its interaction with LPS"

The surge of antimicrobial resistance threatens efficacy of current antibiotics, particularly against Pseudomonas aeruginosa , a highly resistant gram-negative pathogen. The asymmetric outer membrane (OM) of P. aeruginosa combined with its array of efflux pumps provide a barrier to xenobiotic accumulation, thus making antibiotic discovery challenging. We adapted PROSPECT 1 , a target-based, whole-cell screening strategy, to discover small molecule probes that kill P. aeruginosa mutants depleted for essential proteins localized at the OM. We identified BRD1401, a small molecule that has specific activity against a P. aeruginosa mutant depleted for the essential lipoprotein, OprL. Genetic and chemical biological studies identified that BRD1401 acts by targeting the OM β-barrel protein OprH to disrupt its interaction with LPS and increase membrane fluidity. Studies with BRD1401 also revealed an interaction between OprL and OprH, directly linking the OM with peptidoglycan. Thus, a whole-cell, multiplexed screen can identify species-specific chemical probes to reveal novel pathogen biology.

Synthesis, structure, theoretical calculation and antibacterial property of two novel Zn(II)/Ni(II) compounds based on 3, 5-dichlorosalicylaldehyde thiocarbamide ligand

Two new compounds namely [Zn(L1)phen]31 and Ni(L1)phen(MeOH) 2 (L1 = 3, 5-dichlorosalicylaldehyde thiosemicarbazone) were synthesized by the slow evaporation method at room temperature. The structure of ligand L1 was determined using 1H NMR and 13C NMR spectra. X-ray single crystal diffraction analysis revealed that compounds 1-2 can form 3D supramolecular network structures through π···π stacking and hydrogen bonding interactions. The DFT calculation shows that the coordination of ligand and metal is in good agreement with the experimental results. Hirshfeld surface analysis revealed that H…H and Cl…H interactions were the predominant interactions in compounds 1-2. Energy framework analysis indicated that dispersion energy played a dominant role in the energy composition of compounds 1-2. The inhibitory effects of compounds 1-2 against Escherichia coli (E. coli) and Methicillin-resistant Staphylococcus aureus (MRSA) were tested using the paper disk diffusion method (1: E. coli: 18 mm, MRSA: 17 mm, 2: E. coli: 15 mm, MRSA: 16 mm). Ion releasing experiments were conducted to assess the ion release capacity of compounds 1-2 (Zn2+, 4 days, 38.33 µg/mL; Ni2+, 4 days, 29.12 µg/mL). Molecular docking demonstrated the interaction modes of compounds 1-2 with UDP-N-acetylenolpyruvoylglucosamine reductase (MurB) and dihydrofolate reductase (DHFR) in bacteria, involving hydrophobic, stacking, hydrogen bonding and halogen bonding interactions. The generation of reactive oxygen species (ROS) in bacteria under the presence of compounds 1-2 were evaluated using a fluorescent dye known as dichlorodihydrofluorescein diacetate (DCFH-DA). Potential antibacterial mechanisms of compounds 1-2 were proposed.

Identification of terpenoids as dihydropteroate synthase and dihydrofolate reductase inhibitors through structure-based virtual screening and molecular dynamic simulations

Bacterial infections are rising, and antimicrobial resistance (AMR) in bacteria has worsened the scenario, requiring extensive research to find alternative therapeutic agents. Terpenoids play an essential role in protecting plants from herbivores and pathogens. The present study was designed to focus on in silico evaluation of terpenoids for their affinity towards two necessary enzymes, i.e. DHFR and DHPS, which are involved in forming 5, 6, 7, 8-tetrahydrofolate, a key component in bacterial DNA synthesis proteins. Additionally, to account for activity against resistant bacteria, their affinity towards the L28R mutant of DHFR was also assessed in the study. The structure-based drug design approach was used to screen the compound library of terpenes for their interaction with active sites of DHFR and DHPS. Further, compounds were screened based on their dock score, pharmacokinetic properties, and binding affinities. A total of five compounds for each target protein were screened, having dock scores better than their respective standard drug molecules. CNP0169378 (-8.4 kcal/mol) and CNP0309455 (-6.5 kcal/mol) have been identified as molecules with a higher affinity toward the targets of DHFR and DHPS, respectively. At the same time, one molecule CNP0298407 (-5.8 kcal/mol for DHPS, -7.6 kcal/mol for DHFR, -6.1 kcal/mol for the L28R variant), has affinity for both proteins (6XG5 and 6XG4). All the molecules have good pharmacokinetic properties. We further validated the docking study by binding free energy calculations using the MM/GBSA approach and molecular dynamics simulations.Communicated by Ramaswamy H. Sarma.

Discovery of novel tetrahydrobenzothiophene derivatives as MSBA inhibitors for antimicrobial agents

The incidence of infections caused by drug-resistant bacteria has been one of the most serious health threats in the past and is substantially increasing in an alarming rate. Therefore, the development of new antimicrobial agents to combat bacterial resistance effectively is urgent. This study focused on the design and synthesis of 40 novel tetrahydrobenzothiophene amide/sulfonamide derivatives and their antibacterial activities were evaluated. Compounds 2p, 6p, and 6 s exhibited significant inhibitory effects on the growth of bacteria. To assess their safety, the cytotoxicity of the compounds was assessed using human normal liver cells, revealing that compound 6p has lower cytotoxicity. A mouse wound healing experiment demonstrated that compound 6p effectively improved wound infection induced by trauma and accelerated the healing process. Compound 6p holds promise as a potential therapeutic agent for combating bacterial infections.

Dual-target inhibitors based on COX-2: a review from medicinal chemistry perspectives

Inhibitors of COX-2 constitute a class of anti-inflammatory analgesics, showing potential against certain types of cancer. However, such inhibitors are associated with cardiovascular toxicity. Moreover, although single-target molecules possess specificity for particular targets, they often lead to poor safety, low efficacy and drug resistance due to compensatory mechanisms. A new generation of dual-target drugs that simultaneously inhibit COX-2 and another target is showing strong potential to treat cancer or reduce adverse cardiac effects. The present perspective focuses on the structure and functions of COX-2, and its role as a therapeutic target. It also explores the current state and future possibilities for dual-target strategies from a medicinal chemistry perspective.

Using biologically synthesized TiO2 nanoparticles as potential remedy against multiple drug resistant Staphylococcus aureus of bovine mastitis

Presently, there is considerable emphasis on biological synthesis of nanoparticles containing bioactive reducing compounds with an aim to mitigate the harmful effects of pollutants. The approach under study is simple and ideal for the production of durable antimicrobial nanomaterials by novel single-step green synthesis of TiO2 metal oxide nanostructures using ginger and garlic crude aqueous extracts with bactericidal and catalytic activity. A variety of experimental techniques were used to characterize the synthesized nanomaterials. As demonstrated using x-ray diffraction and ultra-violet visible spectroscopy, the produced nanoparticles exhibited high absorption at 318 nm with size varying between 23.38 nm for ginger and 58.64 nm for garlic in biologically-reduced TiO2. At increasing concentrations (500, 1000 µg/50 µl), nanoparticles reduced with garlic exhibited enhanced bactericidal efficacy against multiple drug-resistant S. aureus and effectively decomposed toxic methylene blue (MB) dye. In conclusion, biologically-reduced TiO2 nanoparticles may prove an effective tool in the fight against microbial illnesses and drug resistance.

In Silico Studies of Four Compounds of Cecropia obtusifolia against Malaria Parasite

Malaria is a disease that affects many people in the world. In Mexico, malaria remains an active disease in certain regions, particularly in the states of Chiapas and Chihuahua. While antimalarial effects have been attributed to some species of Cecropia in various countries, no such studies have been conducted in Mexico. Therefore, the objective of this study was to evaluate the in silico antimalarial activity of some active compounds identified according to the literature in the species of Cecropia obtusifolia, belonging to the Cecropiaceae family, such as ursolic acid, α-amyrin, chrysin, and isoorientin. These compounds were evaluated with specific molecular docking and molecular dynamics (MD) studies using three different malarial targets with the PDB codes 1CET, 2BL9, and 4ZL4 as well as the prediction of their pharmacokinetic (Pk) properties. Docking analysis revealed the following best binding energies (kcal/mol): isoorientin-1CET (-9.1), isoorientin-2BL9 (-8.8), and chrysin-4ZL4 (-9.6). MD simulation validated the stability of the complexes. Pharmacokinetics analysis suggested that the compounds would generally perform well if administered. Therefore, these results suggest that these compounds may be used as potential drugs for the treatment of malaria.

"Influence of plasmids, selection markers and auxotrophic mutations on Haloferax volcanii cell shape plasticity"

Haloferax volcanii and other Haloarchaea can be pleomorphic, adopting different shapes, which vary with growth stages. Several studies have shown that H. volcanii cell shape is sensitive to various external factors including growth media and physical environment. In addition, several studies have noticed that the presence of a recombinant plasmid in the cells is also a factor impacting H. volcanii cell shape, notably by favoring the development of rods in early stages of growth. Here we investigated the reasons for this phenomenon by first studying the impact of auxotrophic mutations on cell shape in strains that are commonly used as genetic backgrounds for selection during strain engineering (namely: H26, H53, H77, H98, and H729) and secondly, by studying the effect of the presence of different plasmids containing selection markers on the cell shape of these strains. Our study showed that most of these auxotrophic strains have variation in cell shape parameters including length, aspect ratio, area and circularity and that the plasmid presence is impacting these parameters too. Our results indicated that ΔhdrB strains and hdrB selection markers have the most influence on H. volcanii cell shape, in addition to the sole presence of a plasmid. Finally, we discuss limitations in studying cell shape in H. volcanii and make recommendations based on our results for improving reproducibility of such studies.

Quinoline Hydrazone Derivatives as New Antibacterials against Multidrug Resistant Strains

To develop novel antimicrobial agents a series of 2(4)-hydrazone derivatives of quinoline were designed, synthesized and tested. QSAR models of the antibacterial activity of quinoline derivatives were developed by the OCHEM web platform using different machine learning methods. A virtual set of quinoline derivatives was verified with a previously published classification model of anti-E. coli activity and screened using the regression model of anti-S. aureus activity. Selected and synthesized 2(4)-hydrazone derivatives of quinoline exhibited antibacterial activity against the standard and antibiotic-resistant S. aureus and E. coli strains in the range from 15 to 30 mm by the diameter of growth inhibition zones. Molecular docking showed the complex formation of the studied compounds into the catalytic domain of dihydrofolate reductase with an estimated binding affinity from -8.4 to -9.4 kcal/mol.

Exploration of Remarkably Potential Multitarget-Directed N-Alkylated-2-(substituted phenyl)-1H-benzimidazole Derivatives as Antiproliferative, Antifungal, and Antibacterial Agents

Improving lipophilicity for drugs to penetrate the lipid membrane and decreasing bacterial and fungal coinfections for patients with cancer pose challenges in the drug development process. Here, a series of new N-alkylated-2-(substituted phenyl)-1H-benzimidazole derivatives were synthesized and characterized by 1H and 13C NMR, FTIR, and HRMS spectrum analyses to address these difficulties. All the compounds were evaluated for their antiproliferative, antibacterial, and antifungal activities. Results indicated that compound 2g exhibited the best antiproliferative activity against the MDA-MB-231 cell line and also displayed significant inhibition at minimal inhibitory concentration (MIC) values of 8, 4, and 4 μg mL-1 against Streptococcus faecalis, Staphylococcus aureus, and methicillin-resistant Staphylococcus aureus compared with amikacin. The antifungal data of compounds 1b, 1c, 2e, and 2g revealed their moderate activities toward Candida albicans and Aspergillus niger, with MIC values of 64 μg mL-1 for both strains. Finally, the molecular docking study found that 2g interacted with crucial amino acids in the binding site of complex dihydrofolate reductase with nicotinamide adenine dinucleotide phosphate.

Facile Synthesis of Vanadium Oxide/Carbon Spheres-Doped Nickel Oxide Functioned as a Nanocatalyst and Bactericidal Behavior with Molecular Docking Analysis

Vanadium oxide (V₂O₅) and carbon spheres (Cs)-doped NiO₂ nanostructures (NSs) were prepared using the co-precipitation approach. Several spectroscopic and microscopic techniques, including X-ray diffraction (XRD), UV-vis, FTIR, TEM, and HR-TEM investigations, were used to describe the as-synthesized NSs. The XRD pattern exhibited the hexagonal structure, and the crystallite size of pristine and doped NSs was calculated as 29.3, 32.8, 25.79, and 45.19 nm, respectively. The control sample (NiO₂) showed maximum absorption at 330 nm, and upon doping, a redshift was observed, leading to decreased band gap energy from 3.75 to 3.59 eV. TEM of NiO₂ shows agglomerated nonuniform nanorods exhibited with various nanoparticles without a specific orientation; a higher agglomeration was observed upon doping. The (4 wt %) V₂O₅/Cs-doped NiO₂ NSs served as superior catalysts with a 94.21% MB reduction in acidic media. The significant antibacterial efficacy was estimated against Escherichia coli by measuring the zone of inhibition (3.75 mm). Besides their bactericidal analysis, V₂O₅/Cs-doped NiO₂ was shown to have a binding score of 6.37 for dihydrofolate reductase and a binding score of 4.31 for dihydropteroate synthase in an in silico docking study of E. coli.

Thiophene-Derived Schiff Base Complexes: Synthesis, Characterization, Antimicrobial Properties, and Molecular Docking

Novel thiophene-derived Schiff base ligand DE, where DE is (E)-N¹,N¹-diethyl-N²-(thiophen-2-ylmethylene)ethane-1,2-diamine, and the corresponding M(II) complexes, [M(DE)X₂] (M = Cu or Zn, X = Cl; M = Cd, X = Br), were prepared and structurally characterized. X-ray diffraction studies revealed that the geometry around the center of the M(II) complexes, [Zn(DE)Cl₂] and [Cd(DE)Br₂], could be best described as a distorted tetrahedral. In vitro antimicrobial screening of DE and its corresponding M(II) complexes, [M(DE)X₂], was performed. The complexes were more potent and showed higher activities against Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa, fungi Candida albicans, and protozoa Leishmania major compared to the ligand. Among the studied complexes, [Cd(DE)Br₂] exhibited the most promising antimicrobial activity against all the tested microbes compared to its analogs. These results were further supported by molecular docking studies. We believe that these complexes may significantly contribute to the efficient designing of metal-derived agents to treat microbial infections.

Metabolism and Tissue Elimination of Diaveridine in Swine, Chickens, and Rats Using Radioactive Tracing Coupled with LC-ESI-IT-TOF/MS

Diaveridine (DVD) has widespread use in food animals due to its antibacterial synergistic effects. This study revealed the metabolism, excretion, and tissue elimination of DVD in swine, chickens, and rats following oral gavage of 10 mg/kg b.w. tritium-labeled DVD using radioactive tracing coupled with liquid chromatography-electron spray ionization-ion trap-time-of-flight-mass spectrometry (LC-ESI-IT-TOF/MS). The metabolic pathways involved demethylation, α-hydroxylation, glucuronidation, and sulfonylation and produced four metabolites in swine (M0, DVD; M1, 3'/4'-demethyl-DVD; M2, 3'/4'-demethyl-DVD-O-glucuronide; M4, 2/4-glucuronidated-DVD) and five in chickens (M0∼M2; M3, α-hydroxy-DVD; M4) and rats (M0∼M3; M5, 3'/4'-demethyl-DVD-O-sulfation). M0 was dominant in the excreta of chicken and female and male rats, while M2 was mainly excreted in swine. Among the three species studied, M0 was the most persistent in the kidneys (t_1/2 3.15-3.89 d); therefore, M0 kidney levels are residue monitoring targets. This study enabled a thorough comprehension of the metabolism and pharmacokinetic characteristics of DVD in animals.

Identification of Efflux Substrates Using a Riboswitch-Based Reporter in Pseudomonas aeruginosa

Pseudomonas aeruginosa is intrinsically resistant to many classes of antibiotics, reflecting the restrictive nature of its outer membrane and the action of its numerous efflux systems. However, the dynamics of compound uptake, retention, and efflux in this bacterium remain incompletely understood. Here, we exploited the sensor capabilities of a Z-nucleotide-sensing riboswitch to create an experimental system able to identify physicochemical and structural properties of compounds that permeate the bacterial cell, avoid efflux, and perturb the folate cycle or de novo purine synthesis. In the first step, a collection of structurally diverse compounds enriched in antifolate drugs was screened for ZTP (5-aminoimidazole-4-carboxamide riboside 5'-triphosphate) riboswitch reporter activity in efflux-deficient P. aeruginosa, allowing us to identify compounds that entered the cell and disrupted the folate pathway. These initial hits were then rescreened using isogenic efflux-proficient bacteria, allowing us to separate efflux substrates from efflux avoiders. We confirmed this categorization by measuring intracellular levels of select compounds in the efflux-deficient and -proficient strain using high-resolution liquid chromatography-mass spectrometry (LC-MS). This simple yet powerful method, optimized for high-throughput screening, enables the discovery of numerous permeable compounds that avoid efflux and paves the way for further refinement of the physicochemical and structural rules governing efflux in this multidrug-resistant Gram-negative pathogen. IMPORTANCE Treatment of Pseudomonas aeruginosa infections has become increasingly challenging. The development of novel antibiotics against this multidrug-resistant bacterium is a priority, but many drug candidates never achieve effective concentrations in the bacterial cell due to its highly restrictive outer membrane and the action of multiple efflux pumps. Here, we develop a robust and simple reporter system in P. aeruginosa to screen chemical libraries and identify compounds that either enter the cell and remain inside or enter the cell and are exported by efflux systems. This approach enables the development of rules of compound uptake and retention in P. aeruginosa that will lead to more rational design of novel antibiotics.

Identification of efflux substrates using a riboswitch-based reporter in Pseudomonas aeruginosa

Pseudomonas aeruginosa is intrinsically resistant to many classes of antibiotics, reflecting the restrictive nature of its outer membrane and the action of its numerous efflux systems. However, the dynamics of compound uptake, retention and efflux in this bacterium remain incompletely understood. Here, we exploited the sensor capabilities of a Z-nucleotide sensing riboswitch to create an experimental system able to identify physicochemical and structural properties of compounds that permeate the bacterial cell, avoid efflux, and perturb the folate cycle or de novo purine synthesis. In a first step, a collection of structurally diverse compounds enriched in antifolate drugs was screened for ZTP riboswitch reporter activity in efflux-deficient P. aeruginosa , allowing us to identify compounds that entered the cell and disrupted the folate pathway. These initial hits were then rescreened using isogenic efflux-proficient bacteria, allowing us to separate efflux substrates from efflux avoiders. We confirmed this categorization by measuring intracellular levels of select compounds in the efflux-deficient and - proficient strain using high resolution LC-MS. This simple yet powerful method, optimized for high throughput screening, enables the discovery of numerous permeable compounds that avoid efflux and paves the way for further refinement of the physicochemical and structural rules governing efflux in this multi-drug resistant Gram-negative pathogen.

Importance

Treatment of Pseudomonas aeruginosa infections has become increasingly challenging. The development of novel antibiotics against this multi-drug resistant bacterium is a priority, but many drug candidates never achieve effective concentrations in the bacterial cell due due to its highly restrictive outer membrane and the action of multiple efflux pumps. Here, we develop a robust and simple reporter system in P. aeruginosa to screen chemical libraries and identify compounds that either enter the cell and remain inside, or enter the cell and are exported by efflux systems. This approach enables developing rules of compound uptake and retention in P. aeruginosa that will lead to more rational design of novel antibiotics.

Toward Efficient Bactericidal and Dye Degradation Performance of Strontium- and Starch-Doped Fe2O3 Nanostructures: In Silico Molecular Docking Studies

In this study, various concentrations of strontium (Sr) into a fixed amount of starch (St) and Fe2O3 nanostructures (NSs) were synthesized with the co-precipitation approach to evaluate the antibacterial and photocatalytic properties of the concerned NSs. The study aimed to synthesize nanorods of Fe2O3 with co-precipitation to enhance the bactericidal behavior with dopant-dependent Fe2O3. Advanced techniques were utilized to investigate the structural characteristics, morphological properties, optical absorption and emission, and elemental composition properties of synthesized samples. Measurements via X-ray diffraction confirmed the rhombohedral structure for Fe2O3. Fourier-transform infrared analysis explored the vibrational and rotational modes of the O-H functional group and the C=C and Fe-O functional groups. The energy band gap of the synthesized samples was observed in the range of 2.78-3.15 eV, which indicates that the blue shift in the absorption spectra of Fe2O3 and Sr/St-Fe2O3 was identified with UV-vis spectroscopy. The emission spectra were obtained through photoluminescence spectroscopy, and the elements in the materials were determined using energy-dispersive X-ray spectroscopy analysis. High-resolution transmission electron microscopy micrographs showed NSs that exhibit nanorods (NRs), and upon doping, agglomeration of NRs and nanoparticles was observed. Efficient degradations of methylene blue increased the photocatalytic activity in the implantation of Sr/St on Fe2O3 NRs. The antibacterial potential for Escherichia coli and Staphylococcus aureus was measured against ciprofloxacin. E. coli bacteria exhibit inhibition zones of 3.55 and 4.60 mm at low and high doses, respectively. S. aureus shows the measurement of inhibition zones for low and high doses of prepared samples at 0.47 and 2.40 mm, respectively. The prepared nanocatalyst showed remarkable antibacterial action against E. coli bacteria rather than S. aureus at high and low doses compared to ciprofloxacin. The best-docked conformation of the dihydrofolate reductase enzyme against E. coli for Sr/St-Fe2O3 showed H-bonding interactions with Ile-94, Tyr-100, Tyr-111, Trp-30, ASP-27, Thr-113, and Ala-6.

Unveiling the Efficacy of Sesquiterpenes from Marine Sponge Dactylospongia elegans in Inhibiting Dihydrofolate Reductase Using Docking and Molecular Dynamic Studies

Dihydrofolate reductase (DHFR) is a crucial enzyme that maintains the levels of 5,6,7,8-tetrahydrofolate (THF) required for the biological synthesis of the building blocks of DNA, RNA, and proteins. Over-activation of DHFR results in the progression of multiple pathological conditions such as cancer, bacterial infection, and inflammation. Therefore, DHFR inhibition plays a major role in treating these illnesses. Sesquiterpenes of various types are prime metabolites derived from the marine sponge Dactylospongia elegans and have demonstrated antitumor, anti-inflammation, and antibacterial capacities. Here, we investigated the in silico potential inhibitory effects of 87 D. elegans metabolites on DHFR and predicted their ADMET properties. Compounds were prepared computationally for molecular docking into the selected crystal structure of DHFR (PDB: 1KMV). The docking scores of metabolites 34, 28, and 44 were the highest among this series (gscore values of -12.431, -11.502, and -10.62 kcal/mol, respectively), even above the co-crystallized inhibitor SRI-9662 score (-10.432 kcal/mol). The binding affinity and protein stability of these top three scored compounds were further estimated using molecular dynamic simulation. Compounds 34, 28, and 44 revealed high binding affinity to the enzyme and could be possible leads for DHFR inhibitors; however, further in vitro and in vivo investigations are required to validate their potential.

Phytochemical constituents of Inula britannica as potential inhibitors of dihydrofolate reductase: A strategic approach against shigellosis

Shigella dysenteriae type 1 is considered as an epidemic in different developing countries, which is responsible for the most severe form of bacterial dysentery. It habitually can develop to the most severe form of dysentery with deadly complications. Development of drugs against this disease is still ongoing. Therefore, we used in silico studies to screen the Inula britannica phytocompounds that are used in traditional Chinese and Kampo Medicines and have activities against different diseases. Spinacetin, eupatin, chrysoeriol and diosmetin were successfully passed through the docking-based screening and absorption, distribution, metabolism, excretion and toxicity (ADMET) filtration. The estimated docking affinities of eupatin, diosmetin, chrysoeriol and spinacetin with Dihydrofolate reductase type 1 (DHFR-1), were -6.5, -6.5, -6.3 and -6.1 kcal/mol, respectively. Which were selected for further investigations based on their favorable ADME/Tox characteristics. Then, the 100 ns molecular dynamics (MD) simulations of apo DHFR, spinacetin-DHFR, eupatin-DHFR, chrysoeriol-DHFR and diosmetin-DHFR complexes were carried out. The RMSD fluctuations of the spinacetin, eupatin, chrysoeriol and diosmetin inside the binding site were explored. Subsequently, the effect of binding Spinacetin, eupatin, chrysoeriol and diosmetin upon the dynamic stability of protein was assessed. Additionally, Principal Component Analysis (PCA) and Hydrogen bond analysis was performed for the apo protein and the protein ligand complexes. The results revealed that chrysoeriol and eupatin has good inhibitory effects against DHFR-1 as treatment for Shigella dysenteriae type when compared to other compounds under study. Hence this study implies that eupatin and chrysoeriol are a significantly potential drug like molecule for the treatment of Shigellosis and must undergo validation through in vivo and in vitro experiments.Communicated by Ramaswamy H. Sarma.

Experimental and theoretical study on the regioselective bis- or polyalkylation of 6-amino-2-mercapto-3H-pyrimidin-4-one using zeolite nano-gold catalyst and a quantum hybrid computational method

The synthetic utility of 6-amino-2-mercapto-3H-pyrimidin-4-one 3 as building blocks for new poly (pyrimidine) by alkylation using the bis(halo) compounds and zeolite nano-gold as a catalyst was investigated. Furthermore, the experimental findings by the theoretical Density functional theory (DFT) computations at the DFT/B3LYP level of theory, utilizing the 6-311++G (d,p) basis set in the gas phase, were used to investigate the distinct phases for Regio isomer 11a & 12a and 11b & 12b compounds was fair and of good quality. The stability of the 12a and 12b phases is higher than the other Regio isomer 11a and 11b phases, according to DFT modelling. By computing HOMO and LUMO pictures, the electronic parameters: dipole moment of these compounds in the ground state were theoretically investigated. Non-linear optical (NLO) characteristics and quantum chemical parameters were examined using frontier molecular orbital (FMO) analysis. Natural bond orbital analysis was used to characterize the charge transfer of the electron density in the investigated compounds (NBO). The molecular electrostatic potential surfaces (MEPS) plots have been generated, and absorption spectral analysis in different solvents has been theoretically and experimentally examined to better understand the reactivity spots. At the B3LYP/6-311G (d,p) level of theory, thermodynamic properties were also calculated. Finally, DFT calculations were used to connect the structure-activity relationship (SAR) with real antibacterial results for compounds 12a and 12b.

Molybdenum-doped iron oxide nanostructures synthesized via a chemical co-precipitation route for efficient dye degradation and antimicrobial performance: in silico molecular docking studies

In this research, various concentrations of molybdenum (2, 4 and 6 wt%) doped Fe₃O₄ nanostructures (Mo-Fe₃O₄ NSs) were prepared via a co-precipitation technique. Various techniques were then used to investigate the optical, morphological and structural properties of the NSs in the presence of the dopant materials. X-ray diffraction (XRD) was used to investigate the crystalline nature of the prepared NSs and confirm the orthorhombic and tetragonal structure of Fe₃O₄, with a decrease in crystallinity and crystallite sizes of 36.11, 38.45, 25.74 and 24.38 nm with increasing concentration of Mo (2, 4 and 6%). Fourier-transform infrared (FTIR) spectroscopy analysis was carried out to examine the functional groups in the NSs. Structure, surface morphology and topography were examined via field emission scanning electron microscopy (FE-SEM) and transmission electron microscopy (TEM), which confirmed the fabrication of nanoparticles and nanorods and a floccule-like morphology with a higher doping concentration and the interlayer d-spacing was calculated using high-resolution (HR)TEM, the results of which were a good match to the XRD data. The presence of Mo, Fe and O in a lattice of Mo (2, 4 and 6%) doped Fe₃O₄ was confirmed by energy dispersive X-ray spectroscopy (EDS) analysis. The energy band gap (E _g) was measured via the optical analysis of pure and doped samples, showing a decrease from 2.76 to 2.64 eV. The photoluminescence (PL) spectra exhibit a higher charge combination rate of electron-hole pairs with a higher concentration of doping. The NSs exhibited excellent catalytic activity (CA) in degrading methylene blue (MB) dye in a basic medium by around 86.25%. Additionally, the antimicrobial activity was tested against Escherichia coli (E. coli) bacteria. Pairs of electrons and holes are the fundamental basis for generating reactive oxygen species that kill bacteria. The significant inhibition zones were calculated against E. coli bacteria at around 3.45 mm compared to ciprofloxacin. In silico docking investigations of the Mo-Fe₃O₄ NSs for dihydropteroate synthase (DHPS, binding score: 6.16 kcal mol^-1), dihydrofolate reductase (DHFR, binding score: 6.01 kcal mol^-1), and β-ketoacyl-acyl carrier protein synthase III (FabH, binding score: 5.75 kcal mol^-1) of E. coli show the suppression of the aforementioned enzymes as a potential mechanism besides their microbicidal assay.

Dihydrofolate reductase-like protein inactivates hemiaminal pharmacophore for self-resistance in safracin biosynthesis

Dihydrofolate reductase (DHFR), a housekeeping enzyme in primary metabolism, has been extensively studied as a model of acid-base catalysis and a clinic drug target. Herein, we investigated the enzymology of a DHFR-like protein SacH in safracin (SAC) biosynthesis, which reductively inactivates hemiaminal pharmacophore-containing biosynthetic intermediates and antibiotics for self-resistance. Furthermore, based on the crystal structure of SacH-NADPH-SAC-A ternary complexes and mutagenesis, we proposed a catalytic mechanism that is distinct from the previously characterized short-chain dehydrogenases/reductases-mediated inactivation of hemiaminal pharmacophore. These findings expand the functions of DHFR family proteins, reveal that the common reaction can be catalyzed by distinct family of enzymes, and imply the possibility for the discovery of novel antibiotics with hemiaminal pharmacophore.

Hantzsch-Like Synthesis, DNA Photocleavage, DNA/BSA Binding, and Molecular Docking Studies of Bis(sulfanediyl)bis(tetrahydro-5-deazaflavin) Analogs Linked to Naphthalene Core

The cyclocondensation reaction of aldehydes with dimedone and bis(6-aminopyrimidin-4-one) in acetic acid led to the formation of the corresponding bis(pyrimido[4,5-b]quinoline-4,6-diones) which are known as bis(sulfanediyl)bis(tetrahydro-5-deazaflavin) analogs in a single step. Also, bis(pyrimido[4,5-b]quinoline-4,6-diones) which are linked to naphthyl core via phenoxymethyl linkage is prepared. The interactions of the synthesized compounds with DNA and bovine serum albumin (BSA) were studied. Gel electrophoresis assay was used to show the capability of the compounds to photocleave the supercoiled pBR322 plasmid DNA in UV-A (365 nm). Besides, the most photocleavable compound, bis(tetrahydropyrimido[4,5-b]quinoline-4,6-dione) linked to pyridin-3-yl at position-5 exhibits good binding affinities toward CT-DNA and BSA as supported by UV/VIS spectral studies. In addition to the experimental findings, a molecular docking simulation was performed to collect detailed binding data for this compound to both biomolecules.

Evaluating the accuracy of the AMBER protein force fields in modeling dihydrofolate reductase structures: misbalance in the conformational arrangements of the flexible loop domains

Protein flexible loop regions were once thought to be simple linkers between other more functional secondary structural elements. However, as it becomes clearer that these loop domains are critical players in a plethora of biological processes, accurate conformational sampling of 3D loop structures is vital to the advancement of drug design techniques and the overall growth of knowledge surrounding molecular systems. While experimental techniques provide a wealth of structural information, the resolution of flexible loop domains is sometimes low or entirely absent due to their complex and dynamic nature. This highlights an opportunity for de novo structure prediction using in silico methods with molecular dynamics (MDs). This study evaluates some of the AMBER protein force field's (ffs) ability to accurately model dihydrofolate reductase (DHFR) conformations, a protein complex characterized by specific arrangements and interactions of multiple flexible loops whose conformations are determined by the presence or absence of bound ligands and cofactors. Although the AMBER ffs, including ff19SB, studied well model most protein structures with rich secondary structure, results obtained here suggest the inability to significantly sample the expected DHFR loop-loop conformations - of the six distinct protein-ligand systems simulated, a majority lacked consistent stabilization of experimentally derived metrics definitive the three enzyme conformations. Although under-sampling and the chosen ff parameter combinations could be the cause, given past successes with these MD approaches for many protein systems, this suggests a potential misbalance in available ff parameters required to accurately predict the structure of multiple flexible loop regions present in proteins.Communicated by Ramaswamy H. Sarma.

Multitarget, Selective Compound Design Yields Potent Inhibitors of a Kinetoplastid Pteridine Reductase 1

The optimization of compounds with multiple targets is a difficult multidimensional problem in the drug discovery cycle. Here, we present a systematic, multidisciplinary approach to the development of selective antiparasitic compounds. Computational fragment-based design of novel pteridine derivatives along with iterations of crystallographic structure determination allowed for the derivation of a structure–activity relationship for multitarget inhibition. The approach yielded compounds showing apparent picomolar inhibition of T. brucei pteridine reductase 1 (PTR1), nanomolar inhibition of L. major PTR1, and selective submicromolar inhibition of parasite dihydrofolate reductase (DHFR) versus human DHFR. Moreover, by combining design for polypharmacology with a property-based on-parasite optimization, we found three compounds that exhibited micromolar EC₅₀ values against T. brucei brucei while retaining their target inhibition. Our results provide a basis for the further development of pteridine-based compounds, and we expect our multitarget approach to be generally applicable to the design and optimization of anti-infective agents.

Rapid determination of 2,4-diaminopyrimidine residues through sample pretreatment using immunomagnetic bead purification along with HPLC-UV

To reduce matrix interference and realize simultaneous detection of multiple homologous compounds (trimethoprim (TMP), diaveridine (DVD), ormetoprim (OMP), baquiloprim (BQP), and aditoprim (ADP) in pig, cattle, chicken, and fish muscles), an immunomagnetic bead (IMB)-based sample purification pretreatment with HPLC-UV was developed. A broad-spectrum monoclonal antibody (mAb, named 14C6) was prepared and conjugated with carboxylic-acid-functionalized magnetic nanoparticles using the active ester method to obtain IMBs for sample purification. The extraction solvent was optimized based on the extraction efficiency. Good linearity was observed for all the five analytes (10-200 μg/kg) with the LOD and LOQ of 5 and 10 μg/kg, respectively. The mean recoveries ranged from 62.5% to 76.9%, while the coefficient of variation was <12.2%. The IMB method afforded greater sample purification and enrichment than those achieved with the SPE column-based conventional method. Hence, the IMB-based sample purification is a useful tool to determine 2,4-diaminopyrimidine residues in edible animal tissues.

Thymidine starvation promotes c-di-AMP-dependent inflammation during pathogenic bacterial infection

Antimicrobials can impact bacterial physiology and host immunity with negative treatment outcomes. Extensive exposure to antifolate antibiotics promotes thymidine-dependent Staphylococcus aureus small colony variants (TD-SCVs), commonly associated with worse clinical outcomes. We show that antibiotic-mediated disruption of thymidine synthesis promotes elevated levels of the bacterial second messenger cyclic di-AMP (c-di-AMP), consequently inducing host STING activation and inflammation. An initial antibiotic screen in Firmicutes revealed that c-di-AMP production was largely driven by antifolate antibiotics targeting dihydrofolate reductase (DHFR), which promotes folate regeneration required for thymidine biosynthesis. Additionally, TD-SCVs exhibited excessive c-di-AMP production and STING activation in a thymidine-dependent manner. Murine lung infection with TD-SCVs revealed STING-dependent elevation of proinflammatory cytokines, causing higher airway neutrophil infiltration and activation compared with normal-colony S. aureus and hemin-dependent SCVs. Collectively, our results suggest that thymidine metabolism disruption in Firmicutes leads to elevated c-di-AMP-mediated STING-dependent inflammation, with potential impacts on antibiotic usage and infection outcomes.

Review on the Synthesis and Therapeutic Potential of Pyrido[2,3-d], [3,2-d], [3,4-d] and [4,3-d]pyrimidine Derivatives

The objective of this review is to list the structures composed of a pyridopyrimidine moiety which have shown a therapeutic interest or have already been approved for use as therapeutics. We consider all the synthetic protocols to prepare these pyridopyrimidine derivatives. The review is organized into four sections, successively pyrido[2,3-d]pyrimidines, pyrido[3,4-d]pyrimidines, pyrido[4,3-d]pyrimidines and pyrido[3,2-d]pyrimidines. For each compound we present the biological activity and the synthetic route reported. To produce this manuscript, the bibliographic research was done using Reaxys and Scifinder for each kind of pyridopyrimidine.

QSAR and Molecular Docking Studies of Pyrimidine–Coumarin–Triazole Conjugates as Prospective Anti-Breast Cancer Agents

Cancer is a life-threatening disease and is the second leading cause of death worldwide. Although many drugs are available for the treatment of cancer, survival outcomes are very low. Hence, rapid development of newer anticancer agents is a prime focus of the medicinal chemistry community. Since the recent past, computational methods have been extensively employed for accelerating the drug discovery process. In view of this, in the present study we performed 2D-QSAR (Quantitative Structure-Activity Relationship) analysis of a series of compounds reported with potential anticancer activity against breast cancer cell line MCF7 using QSARINS software. The best four models exhibited a r² value of 0.99. From the generated QSAR equations, a series of pyrimidine-coumarin-triazole conjugates were designed and their MCF7 cell inhibitory activities were predicted using the QSAR equations. Furthermore, molecular docking studies were carried out for the designed compounds using AutoDock Vina against dihydrofolate reductase (DHFR), colchicine and vinblastine binding sites of tubulin, the key enzyme targets in breast cancer. The most active compounds identified through these computational studies will be useful for synthesizing and testing them as prospective novel anti-breast cancer agents.

In-Vitro Catalytic and Antibacterial Potential of Green Synthesized CuO Nanoparticles against Prevalent Multiple Drug Resistant Bovine Mastitogen Staphylococcus aureus

Nanoparticles prepared from bio-reduction agents are of keen interest to researchers around the globe due to their ability to mitigate the harmful effects of chemicals. In this regard, the present study aims to synthesize copper oxide nanoparticles (CuO NPs) by utilizing root extracts of ginger and garlic as reducing agents, followed by the characterization and evaluation of their antimicrobial properties against multiple drug resistant (MDR) S. aureus. In this study, UV-vis spectroscopy revealed a reduced degree of absorption with an increase in the extract amount present in CuO. The maximum absorbance for doped NPs was recorded around 250 nm accompanying redshift. X-ray diffraction analysis revealed the monoclinic crystal phase of the particles. The fabricated NPs exhibited spherical shapes with dense agglomeration when examined with FE-SEM and TEM. The crystallite size measured by using XRD was found to be within a range of 23.38-46.64 nm for ginger-doped CuO and 26-56 nm for garlic-doped CuO. Green synthesized NPs of ginger demonstrated higher bactericidal tendencies against MDR S. aureus. At minimum and maximum concentrations of ginger-doped CuO NPs, substantial inhibition areas for MDR S. aureus were (2.05-3.80 mm) and (3.15-5.65 mm), and they were measured as (1.1-3.55 mm) and (1.25-4.45 mm) for garlic-doped NPs. Conventionally available CuO and crude aqueous extract (CAE) of ginger and garlic roots reduced MB in 12, 21, and 38 min, respectively, in comparison with an efficient (100%) reduction of dye in 1 min and 15 s for ginger and garlic doped CuO NPs.

A Comparative Computational Analysis Approach to Predict Significant Protein-Protein Interactions of Human and Vancomycin Resistant Enterococcus faecalis (VRE) to Prioritize Potential Drug Targets

Background:

Various challenges exist in the treatment of infectious diseases due to the significant rise in drug resistance, resulting in the failure of antibiotic treatment. As a consequence, a dire need has arisen for the rethinking of the drug discovery cycle because of the challenge of drug resistance. The underlying cause of the infectious diseases depends upon associations within the Host-pathogen Protein- Protein Interactions (HP-PPIs) network, which represents a key to unlock new pathogenesis mechanisms. Hence, the elucidation of significant PPIs is a promising approach for the identification of potential drug targets.

Objective:

Identification of the most significant HP-PPIs and their partners, and targeting them to prioritize potential new drug targets against Vancomycin-resistant Enterococcus faecalis (VRE).

Methods:

We applied a computational approach based on one of the emerging techniques i.e. Interolog methodology to predict the significant Host-Pathogen PPIs. Structure-Based Studies were applied to model shortlisted protein structures and validate them through PSIPRED, PROCHECK, VERIFY3D, and ERRAT tools. Furthermore, 18,000 drug-like compounds from the ZINC library were docked against these proteins to study protein-chemical interactions using the AutoDock based molecular docking method.

Results:

The study resulted in the identification of 118 PPIs for Enterococcus faecalis, and prioritized two novel drug targets i.e. Exodeoxyribonuclease (ExoA) and ATP-dependent Clp protease proteolytic subunit (ClpP). Consequently, the docking program ranked 2,670 and 3,154 compounds as potential binders against Exodeoxyribonuclease and ATP-dependent Clp protease proteolytic subunit, respectively.

Conclusion:

Thereby, the current study enabled us to identify and prioritize potential PPIs in VRE and their interacting proteins in human hosts along with the pool of novel drug candidates.

Multicomponent Crystal of Trimethoprim and Citric Acid: Solid State Characterization and Dissolution Rate Studies

BACKGROUND: Trimethoprim is a broad spectrum antimicrobial agent with low solubility in water which causes low bioavailability in systemic circulation. AIM: The purpose of this study was to prepare multicomponent crystals of trimethoprim and citric acid to increase the solubility and dissolution rate of trimethoprim. MATERIALS AND METHODS: Multicomponent crystals were prepared by solvent evaporation method. Characterizations of multicomponent crystalline solid phase properties were carried out by powder X-ray diffraction (PXRD) analysis, differential scanning calorimetry (DSC), FT-IR spectroscopy, scanning electron microscopy (SEM). Solubility and dissolution rate tests were carried out in aqueous medium. RESULTS: The PXRD characterization results showed a new X-ray diffraction pattern in the multicomponent crystal phase. DSC analysis showed the formation of a new endothermic peak. This indicates the formation of a multicomponent crystal phase between trimethoprim and citric acid. The results of the SEM analysis indicate the formation of a new crystal habit. Solubility of multi-component crystal phase of trimethoprim increased 7 times compared to intact trimethoprim. The dissolution of trimethoprim and multicomponent crystals in 0.1 N HCl medium at 60 minutes was 56.36% and 95.57% and CO2-free distilled water medium was 43.03% and 88.26%, respectively. CONCLUSIONS: From the results of the study, it can be concluded that the multicomponent phase of trimethoprim crystals with citric acid successfully increase the solubility and dissolution rate of trimethoprim significantly.

Isolation of phytochemical constituents from Stevia rebaudiana (Bert.) and evaluation of their anticancer, antimicrobial and antioxidant properties via in vitro and in silico approaches

The current study was designed to isolate and characterize some bioactive secondary metabolites by using repeated chromatographic and spectroscopic techniques, targeting their anticancer, antimicrobial, and antioxidant properties through in vitro and in silico approaches. Six compounds were isolated and analyzed by thin layer chromatographic technique and the compounds were identified as 5-O-caffeoyl quinic acid (1), syringin (2), luteolin (3), apigenin (4), jhanol (5), and jhanidiol (6) based on spectroscopic methods. The cytotoxic effect of each compound was dose-dependent, and compound 1 showed a higher anti-proliferative effect (IC₅₀ = 181.3 μg/ml) than other compounds (compound 2, 4, 5, and 6). Besides, compound 1 showed the most promising antibacterial activity with a zone of inhibition ranges from 12-15 mm against different strains compared to ciprofloxacin (14-22 mm). In contrast, compound 3 exerted the highest scavenging property against DPPH free radical. Finally, the in vitro bioactivities were also supported by molecular docking studies. The computational study demonstrated that the isolated compounds exerted stronger affinity compared to the standard drugs towards the binding sites of dihydrofolate reductase (DHFR), glutathione reductase, and urase oxidase.

Synthesis and antimicrobial activity of aryldiazenyl/arylhydrazono pyrazoles

We report the design, synthesis, and in vitro antimicrobial evaluation of functionalized pyrazoles containing a hydrazono/diazenyl moiety. Among these newly synthesized derivatives, 4-[2-(4-chlorophenyl)hydrazono]-5-methyl-2-[2-(naphthalen-2-yloxy)acetyl]-2,4-dihydro-3 H-pyrazol-3-one is a promising antimicrobial agent against Staphylococcus aureus (minimum inhibitory concentration 0.19 μg mL−1). Structure–activity relationship studies reveal that the electronic environment on the distal phenyl ring has a considerable effect on the antimicrobial potential of the hybrid analogues. Molecular docking studies into the active site of S. aureus dihydrofolate reductase also prove the usefulness of hybridizing a pyrazole moiety with azo and hydrazo groups in the design of new antimicrobial agents.

Evaluation of The Antioxidant, Antimicrobial, and Anticancer Activities of Dicliptera bupleuroides Isolated Compounds Using In Vitro and In Silico Studies

Phytochemical investigation of chloroform fraction (DBC) and ethyl acetate fraction (DBE) of D. bupleuroides (Acanthaceae) resulted in the isolation of β-sitosterol (1) from DBC and vanillic acid (2) from DBE, which were first to be isolated from D. bupleuroides. β-Sitosterol (1) exhibited substantial antioxidant activity (IC₅₀ = 198.87 µg/mL), whereas vanillic acid (2) showed significant antioxidant power (IC₅₀ = 92.68 µg/mL) employing 1,1-diphenyl-2-picrylhydrazyl (DPPH*) radical scavenging capacity assay. Both compounds showed pronounced antimicrobial activity using the agar disc diffusion method, particularly against fungi showing MIC values of 0.182 and 0.02 concerning Candida albicans, respectively, and 0.001 mg/mL regarding Penicillium notatum. They revealed considerable antibacterial activity with MIC values ranging between 0.467 and 0.809 mg/mL. Vanillic acid (2) exhibited substantial anticancer potential displaying 48.67% cell viability at a concentration of 100 μg/mL using MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-Diphenyl-2H-Tetrazolium Bromide) assay concerning HepG2 cell lines. These results were further consolidated by in silico studies on different enzymes, where vanillic acid displayed a high fitting score in the active pockets of DNA-gyrase, dihydrofolate reductase, aminoglycoside nucleotidyltransferase, and β-lactamase. It also inhibited human cyclin-dependent kinase 2 (CDK-2) and DNA topoisomerase II, as revealed by the in silico studies. ADME/TOPKAT (absorption, distribution, metabolism, excretion, and toxicity) prediction showed that vanillic acid exhibited reasonable pharmacodynamic, pharmacokinetic, and toxicity properties and, thus, could perfectly together with D. bupleuroides crude extract be incorporated in pharmaceutical preparations to counteract cancer and microbial invasion, as well as oxidative stress. Thus, it is concluded that D. bupleroides could be a potential source of therapeutically active compounds, which would be helpful for the discovery of clinically effective and safe drugs.

Synthesis, In Silico Prediction and In Vitro Evaluation of Antimicrobial Activity, DFT Calculation and Theoretical Investigation of Novel Xanthines and Uracil Containing Imidazolone Derivatives

Novel xanthine and imidazolone derivatives were synthesized based on oxazolone derivatives 2a-c as a key intermediate. The corresponding xanthine 3-5 and imidazolone derivatives 6-13 were obtained via reaction of oxazolone derivative 2a-c with 5,6-diaminouracils 1a-e under various conditions. Xanthine compounds 3-5 were obtained by cyclocondensation of 5,6-diaminouracils 1a-c with different oxazolones in glacial acetic acid. Moreover, 5,6-diaminouracils 1a-e were reacted with oxazolones 2a-c in presence of drops of acetic acid under fused condition yielding the imidazolone derivatives 6-13. Furthermore, Schiff base of compounds 14-16 were obtained by condensing 5,6-diaminouracils 1a,b,e with 4-dimethylaminobenzaldehyde in acetic acid. The structural identity of the resulting compounds was resolved by IR, 1H-, 13C-NMR and Mass spectral analyses. The novel synthesized compounds were screened for their antifungal and antibacterial activities. Compounds 3, 6, 13 and 16 displayed the highest activity against Escherichia coli as revealed from the IC50 values (1.8-1.9 µg/mL). The compound 16 displayed a significant antifungal activity against Candia albicans (0.82 µg/mL), Aspergillus flavus (1.2 µg/mL) comparing to authentic antibiotics. From the TEM microgram, the compounds 3, 12, 13 and 16 exhibited a strong deformation to the cellular entities, by interfering with the cell membrane components, causing cytosol leakage, cellular shrinkage and irregularity to the cell shape. In addition, docking study for the most promising antimicrobial tested compounds depicted high binding affinity against acyl carrier protein domain from a fungal type I polyketide synthase (ACP), and Baumannii penicillin- binding protein (PBP). Moreover, compound 12 showed high drug- likeness, and excellent pharmacokinetics, which needs to be in focus for further antimicrobial drug development. The most promising antimicrobial compounds underwent theoretical investigation using DFT calculation.

The Complementarity Principle-One More Step towards Analytical Docking on the Example of Dihydrofolate Reductase Complexes

New approaches to assessing the “enzyme–ligand” complementarity, taking into account hydrogens, have been proposed. The approaches are based on the calculation of three-dimensional maps of the electron density of the receptor–ligand complexes. The action of complementarity factors, first proposed in this article, has been demonstrated on complexes of human dihydrofolate reductase (DHFR) with ligands. We found that high complementarity is ensured by the formation of the most effective intermolecular contacts, which are provided due to predominantly paired atomic–atomic interactions, while interactions of the bifurcate and more disoriented type are minimized. An analytical docking algorithm based on the proposed receptor–ligand complementarity factors is proposed.