Computational Approaches to Develop Isoquinoline Based Antibiotics through DNA Gyrase Inhibition Mechanisms Unveiled through Antibacterial Evaluation and Molecular Docking

Anticandidal Effect of New Imidazole Derivatives Over Aspartic Protease Inhibition

Candidiasis is one of the most serious microbial infections in the world. One of the main virulence factors for Candida albicans is the crucial secretion of aspartic proteases (Saps). Saps are hydrolytic enzymes that play a major role in many fungal pathophysiological processes as well as in many levels of the associations between the fungus and its host. In this work, we report on the synthesis, characterization, and anti-candida agent evaluation of a family of 13 imidazolidine-based aspartate protease inhibitors. In vitro and in silico enzyme inhibition studies have confirmed these compounds' ability to inhibit fungal aspartate protease. Based on the molecular mechanistic value scores from molecular docking and MD simulations, we selected the top compounds 5b (binding energy -13.90 kcal/mol) and 5m (binding energy -12.94 kcal/mol) from among 5a-l based on the molecular mechanistic value scores from molecular docking and MD simulations for use in in vitro validations. In the results, imidazolidine derivatives showed strong aspartic protease inhibition activity. In conclusion, compounds 5b and 5m were found as potent anti-candida agents and screened for further pre-clinical and clinical validations.

Synthesis and Evaluation of Biological Activities for a Novel 1,2,3,4-Tetrahydroisoquinoline Conjugate with Dipeptide Derivatives: Insights from Molecular Docking and Molecular Dynamics Simulations

Peptide synthesis has opened new frontiers in the quest for bioactive molecules with limitless biological applications. This study presents the synthesis of a series of novel isoquinoline dipeptides using advanced spectroscopic techniques for characterization. These compounds were designed with the goal of discovering unexplored biological activities that could contribute to the development of novel pharmaceuticals. We evaluated the biological activities of novel compounds including their antimicrobial, antibacterial, and antifungal properties. The results show promising activity against Escherichia coli and potent antibacterial activity against MTCC 443 and MTCC 1688. Furthermore, these compounds demonstrate strong antifungal activity, outperforming existing standard drugs. Computational binding affinity studies of tetrahydroisoquinoline-conjugated dipeptides against E. coli DNA gyrase displayed significant binding interactions and binding affinity, which are reflected in antimicrobial activities of compounds. Our integrative significant molecular findings from both wet and dry laboratories would help pave a path for the development of antimicrobial therapeutics. The findings suggest that these isoquinoline-conjugated dipeptides could be excellent candidates for drug development, with potential applications in the fight against bacterial and fungal infections. This research represents an exciting step forward in the field of peptide synthesis and its potential to discover novel bioactive molecules with significant implications for human health.

Norfloxacin derivatives as DNA gyrase and urease inhibitors: synthesis, biological evaluation and molecular docking

Background: DNA gyrase and urease enzymes are important targets for the treatment of gastroenteritis, appendicitis, tuberculosis, urinary tract infections and Crohn's disease. Materials & methods: Esterification of norfloxacin was performed to enhance DNA gyrase and urease enzyme inhibition potential. Structure elucidation and chemical characterization were done through spectral (1H NMR, Fourier transform IR, 13C NMR) and carbon, hydrogen, nitrogen and sulfur analysis along with molecular docking. Results & conclusion: The majority of derivatives exhibited significant results but the 3e derivative showed maximum bactericidal, DPPH scavenging (96%), DNA gyrase and urease enzyme inhibitory activity with IC50 of 0.15 ± 0.24 and 1.14 ± 0.11 μM respectively which was further supported by molecular docking studies. So, the active derivatives can serve as a lead compound for the treatment of various pathological conditions.

Antibacterial activity of paroxetine against Staphylococcus aureus and possible mechanisms of action

Aim: To evaluate the antibacterial activity of paroxetine alone and associated with oxacillin against isolates of methicillin-sensitive and -resistant Staphylococcus aureus. Materials & methods: The broth microdilution and checkerboard techniques were used, with investigation of possible mechanisms of action through flow cytometry, fluorescence microscopy and molecular docking, in addition to scanning electron microscopy for morphological analysis. Results: Paroxetine showed a MIC of 64 μg/ml and bactericidal activity, mostly additive interactions in combination with oxacillin, evidence of action on genetic material and membrane, morphological changes in microbial cells and influence on virulence factors. Conclusion: Paroxetine has antibacterial potential from the perspective of drug repositioning.

Antibiotic discovery against Piscirickettsia salmonis using a combined in silico and in vitro approach

Piscirickettsia salmonis is one of the main pathogens causing considerable economic losses in salmonid farming. The DNA gyrase of several pathogenic bacteria has been the target of choice for antibiotic design and discovery for years, due to its key function during DNA replication. In this study, we carried out a combined in silico and in vitro approach to antibiotic discovery targeting the GyrA subunit of Piscirickettsia salmonis. The in silico results of this work showed that flumequine (-6.6 kcal/mol), finafloxacin (-7.2 kcal/mol), rosoxacin (-6.6 kcal/mol), elvitegravir (-6.4 kcal/mol), sarafloxacin (-8.3 kcal/mol), orbifloxacin (-7.9 kcal/mol), and sparfloxacin (-7.2 kcal/mol) are docked with good affinities in the DNA binding domain of the Piscirickettsia salmonis GyrA subunit. In the in vitro inhibition assay, it was observed that most of these molecules inhibit the growth of Piscirickettsia salmonis, except for elvitegravir. We believe that this methodology could help to significantly reduce the time and cost of antibiotic discovery trials to combat Piscirickettsia salmonis within the salmonid farming industry.

Combined Bioinformatics and Combinatorial Chemistry Tools to Locate Drug-Able Anti-TB Phytochemicals: A Cost-Effective Platform for Natural Product-Based Drug Discovery

Based on extensive experimental studies, a huge number of phytochemicals showed potential activity against tuberculosis (TB) at a lower minimum inhibitory concentration (MIC) and fewer toxicity profiles. However, these promising drugs have not been able to convert from 'lead' to 'mainstream' due to inadequate drug-ability profiles. Thus, early drug-prospective analyses are required at the primary stage to accelerate natural-product-based drug discovery with limited resources and time. In the present study, we have selected seventy-three potential anti-TB phytochemicals (MIC value ≤10 μg/mL) and assessed the drug-ability profiles using bioinformatics and combinatorial chemistry tools, systematically. Primarily, the molecular docking study was done against two putative drug targets, catalase-peroxidase enzyme (katG) and RNA polymerase subunit-β (rpoB) of Mycobacterium tuberculosis (Mtb) using AutoDock 4.2 software. Further, assessed the drug-ability score from Molsoft, toxicity profiles from ProTox, pharmacokinetics from SwisADME, hierarchical cluster analysis (HCA) by ChemMine tools and frontier molecular orbitals (FMOs) with Avogadro and structural activity relationships (SAR) analysis with ChemDraw 18.0 software. Above analyses indicated that, lower MIC exhibited anti-TB phytochemicals, abietane, 12-demethylmulticaulin exhibited poor docking and drug-ability scores, while tiliacorinine, 2-nortiliacorinine showed higher binding energy and drug-ability profiles. Overall, tiliacorinine, 2-nortiliacorinine, 7α-acetoxy-6β-hydroxyroyleanone (AHR), (2S)-naringenin and isovachhalcone were found as the most active and drug-able anti-TB candidates from 73 candidates. Phytochemicals are always a vital source of mainstream drugs, but the MIC value of a phytochemical is not sufficient for it to be promoted. An ideal drug-ability profile is therefore essential for achieving clinical success, where advanced bioinformatics tools help to assess and analyse that profile. Additionally, several natural pharmacophores found in existing anti-TB drugs in SAR analyses also provide crucial information for developing potential anti-TB drug. As a conclusion, combined bioinformatics and combinatorial chemistry are the most effective strategies to locate potent-cum-drug-able candidates in the current drug-development module.

Analysis of SYK Gene as a Prognostic Biomarker and Suggested Potential Bioactive Phytochemicals as an Alternative Therapeutic Option for Colorectal Cancer: An In-Silico Pharmaco-Informatics Investigation

BACKGROUND

SYK gene regulates the expression of SYK kinase (Spleen tyrosine kinase), an important non-receptor protein-tyrosine kinase for immunological receptor-mediated signaling, which is also considered a tumor growth metastasis initiator. An onco-informatics analysis was adopted to evaluate the expression and prognostic value of the SYK gene in colorectal cancer (CRC), the third most fatal cancer type; of late, it may be a biomarker as another targeted site for CRC. In addition, identify the potential phytochemicals that may inhibit the overexpression of the SYK kinase protein and minimize the human CRC.

MATERIALS & METHODS

The differential expression of the SYK gene was analyzed using several transcriptomic databases, including Oncomine, UALCAN, GENT2, and GEPIA2. The server cBioPortal was used to analyze the mutations and copy number alterations, whereas GENT2, Gene Expression Profiling Interactive Analysis (GEPIA), Onco-Lnc, and PrognoScan were used to examine the survival rate. The protein-protein interaction network of SYK kinase and its co-expressed genes was conducted via Gene-MANIA. Considering the SYK kinase may be the targeted site, the selected phytochemicals were assessed by molecular docking using PyRx 0.8 packages. Molecular interactions were also observed by following the Ligplot+ version 2.2. YASARA molecular dynamics simulator was applied for the post-validation of the selected phytochemicals.

RESULTS

Our result reveals an increased level of mRNA expression of the SYK gene in colorectal adenocarcinoma (COAD) samples compared to those in normal tissues. A significant methylation level and various genetic alterations recurrence of the SYK gene were analyzed where the fluctuation of the SYK alteration frequency was detected across different CRC studies. As a result, a lower level of SYK expression was related to higher chances of survival. This was evidenced by multiple bioinformatics platforms and web resources, which demonstrated that the SYK gene can be a potential biomarker for CRC. In this study, aromatic phytochemicals, such as kaempferol and glabridin that target the macromolecule (SYK kinase), showed higher stability than the controls, and we have estimated that these bioactive potential phytochemicals might be a useful option for CRC patients after the clinical trial.

CONCLUSIONS

Our onco-informatics investigation suggests that the SYK gene can be a potential prognostic biomarker of CRC. On the contrary, SYK kinase would be a major target, and all selected compounds were validated against the protein using in-silico drug design approaches. Here, more in vitro and in vivo analysis is required for targeting SYK protein in CRC.

p-TSA.H2O mediated one-pot, multi-component synthesis of isatin derived imidazoles as dual-purpose drugs against inflammation and cancer

A novel one-pot multicomponent reaction was performed to synthesize different imidazole and benzotriazole (BTA) isatin-based medicinally important compounds using (p-TSA·H₂O) as an economical and operative acid catalyst. The yield of the products was found to be up to a maximum of 92% when using this catalyst. Antioxidant, anti-breast cancer and anti-inflammatory activities of these 13 isatin-based derivatives (named as 5a-m) were assessed. The inhibitory effects of these compounds were tested in vitro against cyclooxygenase-2 (COX-2, an enzyme responsible for inflammation) and phosphoinositide-3 kinase (PI3K, a key enzyme in breast cancer). "Among the 13 isatin-based Imidazole derivatives, five compounds (5a, 5d, 5f, 5 k and 5l) were found to exhibit anti-inflammatory as well as anti-cancer activity, which was validated using HRBC stabilization assay (to show anti-inflammatory activity) and cytotoxicity in MCF-7 (breast cancer cell line) to provide proof for anti-cancer property of the compounds". The molecular interactions between the two enzymes were probed using molecular docking. Structure-Activity Relationship (SAR) and ADMET prediction results were also useful to screen the most effective imidazole derivatives and to establish them as putative COX-2 inhibitors/anti-inflammatory drugs. These selected compounds which showed appreciable activity against COX-2 and PI3K are promising drug candidates for the treatment of breast cancer and inflammation which is often associated with breast cancer pathophysiology.

Anticancer Effects of Novel Tetrahydro-Dimethyl-Xanthene-Diones

BACKGROUND

The derivatives of xanthene are known to have promising anticancer properties, in comparison to xanthene itself.

OBJECTIVE

The object of our study was to develop few xanthene derivatives (a family of fifteen novel 3,4,6,7- tetrahydro-3,3-dimethyl-9-phenyl-2H-xanthene-1,8(5H, 9H)-diones encoded as 4a-4m), which were effectively prepared through regioselective synthesis approach, and to test their anticancer effects.

METHODS

A series of cell lines were used in this study, first to assess the cytotoxicity and then the drug efficacy of target compounds, consecutively. Prior to MTT assay, the compounds were analysed for their antioxidant properties, since oxidative stress is an important factor in the development of many cancer types. The anticancer properties of 4a-m have been assessed over in silico (molecular docking and ADMET assessments) and in vitro (MTT assay) methods.

RESULTS

Compounds 4h and 4i showed a relative percentage anticancer activity of 86.25±1.25 & 89.74±1.64 against BT474 (ER+HER2+), and 90.56±1.18 & 93.24±1.80 against MCF-7 (ER-HER2), respectively.

CONCLUSION

The animal model and pre-clinical studies for 4h and 4i should be performed in order to develop them as future anticancer agents.

Synthesis and discovery of triazolo-pyridazine-6-yl-substituted piperazines as effective anti-diabetic drugs; evaluated over dipeptidyl peptidase-4 inhibition mechanism and insulinotropic activities

A family of 12 triazolo-pyridazine-6-yl-substituted piperazines (5a-l) was synthesized and evaluated for their Dipeptidyl peptidase-4 (DPP-4) inhibition potentials in order to develop them as anti-diabetic medications. In the two-step synthesis process, 6-chloro-3-(m-tolyl)-[1,2,4]triazolo[4,3-b]pyridazine was synthesized with one-pot mode using pyridine, 3,6-dichloropyridazine 5-(3-methyl-phenyl)tetrazole in toluene. Conjugating corresponding 2° amines with 6-chloro-3-(m-tolyl)-[1,2,4]triazolo[4,3-b]pyridazine afforded the target triazolo-pyridazine-6-yl-substituted piperazines (5a-l). DPP-4 inhibition potential of these compounds was testified in silico and in nitro along with their insulinotropic activities in 832/13 INS-1 cells. H₂O₂ radical scavenging assay and MTT assay were conducted to assess the antioxidant and cytotoxicity of these compounds respectively. Molecular docking and ELISA based enzyme inhibition assay results revealed the strong inhibition potential of the target compounds. MTT assay results indicated a maximum dose of 2.5 nM (IC₅₀ 1.25 nM) could be used and above this level vital for the cells. Compounds 5a, 5c, 5g and 5i were found with excellent antioxidant and insulinotropic activity up to 99%.

Synthesis and discovery of pyrazolo-pyridine analogs as inflammation medications through pro- and anti-inflammatory cytokine and COX-2 inhibition assessments

This article briefs about the efforts taken to synthesis, characterize and develop (E)-5-methyl-2-phenyl-3-(thiophen-2-yl)-7-(thiophen-2-ylmethylene)-3,3a,4,5,6,7-hexahydro-2H-pyrazolo[4,3-c]pyridine and their analogs. In the two-step reaction, the first step is the synthesis of (3Z,5E)-1-methyl-3,5-bis(thiophen-2-ylmethylene)piperidin-4-one derivatives (3a-l) by stirring the mixture of 1-methylpiperidin-4-one and substituted thiophene-carbaldehydes in presence of methanol. In the second and final step, compounds 3a-l were refluxed with phenyl-hydrazine to achieve the target compounds (E)-5-methyl-2-phenyl-3-(thiophen-2-yl)-7-(thiophen-2-ylmethylene)-3,3a,4,5,6,7-hexahydro-2H-pyrazolo[4,3-c]pyridine and their analogs (5a-l) in good yield. These compounds were used to assess their inflammation regulation properties in macrophages by executing quantitative pro-inflammatory and anti-inflammatory proteins such as TNF-α, IL-1β, IL6, and IL-10 respectively. In silico and in vitro COX-2 inhibition studies helped to understand the molecular interaction or plausible mechanism during the inflammation regulation that showed by the compounds. In the results, among the 12-member family of pyrazolo-pyridines (5a-l), 5a, 5b, 5g, and 5j were showed excellent in silico binding affinity (1-10 nM), least binding energy (-12.45 to -14.27 kcal/mol) and in vitro COX-2 inhibition (relative percentage activity maximum 96.42%). Thus, these compounds perhaps to be future anti-inflammatory drugs.