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"Mali, N"
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Identification of hydantoin based Decaprenylphosphoryl-β-d-Ribose Oxidase (DprE1) inhibitors as antimycobacterial agents using computational tools
2022
Tuberculosis (TB) is one of the emerging infectious diseases in the world. DprE1 (Decaprenylphosphoryl-β-
d
-ribose 2′-epimerase), an enzyme accountable for mycobacterial cell wall synthesis was the first drug gable target based on discoveries of inhibitors via HTS (high throughput screening). Since then, many literature reports have been published so far enlightening varieties of chemical scaffolds acting as inhibitors of DprE1. Herein, in our present study, we have developed statistically robust GA-MLR (genetic algorithm multiple linear regression), atom-based as well as field based-3D-QSAR models. Both atom-based as well as field based-3D-QSAR models (internally as well as externally validated) were obtained with robust Training set, R
2
> 0.69 and Test set, Q
2
> 0.50. We have also developed top ranked 5 point hypothesis AAAHR_1 among 14 CPHs (common pharmacophore hypotheses). We found that our dataset molecule had more docking score (XP mode = − 9.068 kcal/mol) than the standards isoniazid and ethambutol; when docked into binding pockets of enzyme 4P8C with Glide module. We further queried our best docked dataset molecule 151 for ligand based virtual screening using “
SwissSimilarity
” platform. Among 9 identified hits, we found ZINC12196803 had best binding energies and docking score (docking score = − 9.437 kcal/mol, MMGBSA dgBind = − 70.508 kcal/mol). Finally, our molecular dynamics studies for 1.2–100 ns depicts that these complexes are stable. We have also carried out in-silico ADMET predictions, Cardiac toxicity, ‘SwissTargetPredictions’ and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) binding energy calculations for further explorations of dataset as well as hit molecules. Our current studies showed that the hit molecule ZINC12196803 may enlighten the path for future developments of DprE1 inhibitors.
Journal Article
Silver Nanoparticles (AgNPs) as Potential Antiviral Agents: Synthesis, Biophysical Properties, Safety, Challenges and Future Directions─Update Review
2025
AgNPs have gained significant attention due to their unique physicochemical properties, making them valuable across a range of fields including medicine, textiles, and household products. With their strong antimicrobial and antiviral properties, AgNPs have shown promise in treating infections, particularly in wound care management. This review explores the mechanisms underlying the antiviral activities of AgNPs, as well as the methods used for their synthesis, which include physical, chemical, and biological approaches. The review also addresses the potential limitations of AgNPs, including their cytotoxicity to humans and the environment. The interaction between AgNPs and microorganisms, particularly viruses, varies based on synthesis methods and particle morphology. As viral infections, including resistant strains, present major global health challenges, there is a growing need for alternative antiviral therapies. Metal nanoparticles like AgNPs offer potential advantages over conventional antiviral drugs due to their broad target range, which reduces the likelihood of resistance development. This review highlights AgNPs’ effectiveness against a variety of viruses, such as HIV, hepatitis B, and respiratory syncytial virus, and discusses their potential for use in novel antiviral treatments. The review also examines AgNPs’ toxicity, offering insights into their future therapeutic roles.
Journal Article
Molecular Hybrid Design, Synthesis, In Vitro Cytotoxicity, In Silico ADME and Molecular Docking Studies of New Benzoate Ester-Linked Arylsulfonyl Hydrazones
by
Çakmak, Reşit
,
Akkoc, Senem
,
Başaran, Eyüp
in
A549 Cells
,
Antidepressants
,
Antineoplastic Agents - chemical synthesis
2024
In this paper, we present the synthesis and characterization of two known sulfonyl hydrazides (1 and 2) and their new sulfonyl hydrazone derivatives (9–20), as well as in vitro and in silico investigations of their cytotoxic properties against human lung (A549) and human breast (MCF-7) cancer cell lines. The target compounds (9–20) obtained in high yields were synthesized for the first time by a multi-step reaction, and their structures were confirmed by elemental analysis and various spectral techniques, including FT-IR, 1H-, and 13C-NMR. The antiproliferative profiles of these compounds (1, 2, and 9–20) in this study were determined at concentrations of 200, 100, 50, and 25 µM against selected cancer cell lines for 72 h using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) method. Except for compounds 1 and 2, other compounds (9–20) demonstrated cytotoxic activity at concentrations lower than 200 µM. The newly synthesized compounds (9–20) demonstrated antiproliferative activities at a micromolar level, with IC50 values in the range of 29.59–176.70 μM for the A549 cell line and 27.70–170.30 μM for the MCF-7 cell line. Among these compounds, compound 15 (IC50 = 29.59 μM against A549 cell line and IC50 = 27.70 μM against MCF-7 cell line) showed the highest cytotoxic activity against these two cancer cell lines compared to the reference drug cisplatin (IC50 = 22.42 μM against A549 cell line and IC50 = 18.01 μM against MCF-7 cell line). From docking simulations, to establish a plausible binding mode of compounds, we noticed that compound 15 demonstrated the highest affinity (−6.8508 kcal/mol) for estrogen receptor-beta (ERbeta) compared to others, suggesting promising ERbeta binding potential. Most compounds followed Lipinski’s rule of five, with acceptable logP values. Additionally, all had mixed gastrointestinal absorption and limited blood–brain barrier permeability. Overall, our study proposed new sulfonyl hydrazones as a potential class of anticancer agents.
Journal Article
Design, synthesis, QSAR modelling and molecular dynamic simulations of N-tosyl-indole hybrid thiosemicarbazones as competitive tyrosinase inhibitors
2024
Tyrosinase is an enzyme crucial for the progression of melanogenesis. Immoderate production of melanin may be the cause of hyperpigmentation and darkening leading to skin diseases. Tyrosinase is the most researched target for suppressing melanogenesis since it catalyzes the rate-limiting stage of melanin production. Thiosemicarbazones have been reported to possess strong inhibition capability against tyrosinase. We have designed and synthesized eighteen N-tosyl substituted indole-based thiosemicarbazones as competitive tyrosinase inhibitors in the current work. All the compounds exhibited outstanding to good potency with half maximal inhibitory concentration in the range of 6.40 ± 0.21 µM to 61.84 ± 1.47 µM. The compound
5r
displayed the top-tier inhibition amongst the entire series with IC
50
= 6.40 ± 0.21 µM. Compounds,
5q
and
5r
exhibited competitive inhibitions in concentration dependent manner with Ki = 3.42 ± 0.03 and 10.25 ± 0.08 µM respectively. The binding mode of
5r
was evaluated through in silico molecular dynamics simulations and molecular docking, while ADME assessment studies predicted the drug-like characteristics of the derivatives. The newly synthesized derivatives may serve as a structural guide for designing and developing novel tyrosinase inhibitors.
Journal Article
Theoretical and Anti-Klebsiella pneumoniae Evaluations of Substituted 2,7-dimethylimidazo1,2-apyridine-3-carboxamide and Imidazopyridine Hydrazide Derivatives
by
Anand, Amit
,
Kuznetsov, Aleksey
,
Jawarkar, Rahul D.
in
Anti-Bacterial Agents - chemistry
,
Anti-Bacterial Agents - pharmacology
,
Anti-Infective Agents
2023
A series of multistep synthesis protocols was adopted to synthesize substituted imidazopyridines (IMPs) (SM-IMP-01 to SM-IMP-13, and DA-01-05). All substituted IMPs were then characterized using standard spectroscopic techniques such as 1H-NMR, 13C-NMR, elemental analyses, and mass spectrometry. Our both in vitro qualitative and quantitative results for antibacterial analysis, against Klebsiella pneumoniae ATCC 4352 and Bacillus subtilis ATCC 6051 suggested that all compounds essentially exhibited activity against selected strains of bacteria. Our DFT analyses suggested that the compounds of the SM-IMP-01–SM-IMP-13 series have HOMO/LUMO gaps within 4.43–4.69 eV, whereas the compounds of the DA-01–DA-05 series have smaller values of the HOMO/LUMO gaps, 3.24–4.17 eV. The lowest value of the global hardness and the highest value of the global softness, 2.215 and 0.226 eV, respectively, characterize the compound SM-IMP-02; thus, it is the most reactive compound in the imidazopyridine carboxamide series (except hydrazide series). This compound also depicted lesser MIC values against Klebsiella pneumoniae ATCC 4352 and Bacillus subtilis ATCC 6051 as 4.8 µg/mL, each. In terms of another series, hydrazide DA-05 depicted strong antimicrobial actions (MIC: 4.8 µg/mL against both bacterial strains) and also had the lowest energy gap (3.24 eV), higher softness (0.309 eV), and lesser hardness (1.62 eV). Overall, when we compare qualitative and quantitative antimicrobial results, it is been very clear that compounds with dibromo substitutions on imidazopyridine (IMP) rings would act as better antimicrobial agents than those with -H at the eighth position on the IMP ring. Furthermore, substituents of higher electronegativities would tend to enhance the biological activities of dibromo-IMP compounds. DFT properties were also well comparable to this trend and overall, we can say that the electronic behavior of compounds under investigation has key roles in their bioactivities.
Journal Article
Design, synthesis, in vitro, and in silico studies of 4-fluorocinnamaldehyde based thiosemicarbazones as urease inhibitors
by
Al-Harrasi, Ahmed
,
Shafiq, Zahid
,
Ullah, Saeed
in
4-fluorocinnamaldehyde
,
639/638/309
,
639/638/403
2025
Clinically significant problems such as kidney stones and stomach ulcers are linked to the activation of the urease enzyme. At low pH, this enzyme gives an ideal environment to Helicobacter pylori in the stomach which is the cause of gastric ulcers and peptic ulcers. In recent work, we have developed a library of 4-fluorocinnamaldehyde base thiosemicarbazones and assessed them for their potential against urease enzyme. The synthesized compounds displayed significant to moderate inhibition potential with IC
50
values ranging from 2.7 ± 0.5 µM to 29.0 ± 0.5 µM. compound
3c
displayed the highest inhibition potential followed by
3a
and
3b
. Two compounds of the series
3f
and
3 g
remained inactive against urease. The kinetic study of compound
3c
exhibited a competitive type of inhibition with a
K
i
value of 3.26 ± 0.0048 µM. SAR analysis was also thoroughly done. Molecular docking was used to analyze the interaction pattern of each derivative, and the outcomes demonstrated that the compounds had excellent binding interactions with the active site.
Journal Article
Synthesis, in vitro, and in silico studies of 7-fluorochromone based thiosemicarbazones as α-glucosidase inhibitors
2025
Increased blood sugar is a typical manifestation of Type-2 Diabetes Mellitus (T2DM), a metabolic disorder that can be effectively managed with the help of α-glucosidase inhibitors. A range of new chromone based thiosemicarbazone derivatives (3a-t) was synthesized and assessed due to their ability to suppress α-glucosidase in this research. Having IC
50
values spanning from 6.40 ± 0.15 to 62.81 ± 0.79 μM, the compounds demonstrated strong inhibitory actions. The compound 3 k showed the most inhibitory effect among all of them, by an IC
50
measurement of 6.40 ± 0.15 µM. It was concluded through a structure–activity relationship (SAR) assessment that various substituents on thiosemicarbazone moieties had a significant impact on the differences in α-glucosidase inhibition. Molecular docking experiments provide light on important interactions, including π-π interactions and hydrogen bridges, between compounds and role of the carbothioamide and chromenyl groups in ligand attachment to the critical residues of α-glucosidase. The binding interactions, alignment, stability, and structural arrangement of the prepared molecules in the catalytic pocket of α-glucosidase were explored using in silico strategies such as docking studies, pharmacokinetic analysis, and molecular dynamics simulations. This investigation directed to find compounds with favorable profiles for future progress as potential therapeutic agents for type 2 diabetes. Importantly, when benchmarking against acarbose, the lead candidate showed substantially greater efficacy.
Journal Article
Japanese encephalitis genotype I virus-like particles stably expressed in BHK-21 cells serves as potential antigen in JE IgM ELISA
2022
Japanese encephalitis virus (JEV) is one of the leading causes of epidemic encephalitis in South Asian countries. Due to the short-term viremia, detecting IgM antibodies by ELISA is treated as the front-line diagnostic assay. Co-circulation and multiple exposures to antigenically cross-reactive flaviviruses in India pose a challenge in serodiagnosis. Replacing the whole virus antigen currently used in the JE IgM detection kits (ELISA) may improve the specificity and sensitivity of the existing JE MAC ELISA kits. For this purpose, we developed a stably transfected cell clone, BHK-IE6, which expresses a high amount of VLPs up to 37 µg/ml and is consistent in expression up to 40 passages. For the expression of VLPs in the secretory form, we cloned the JEV G-I prM-E coding gene along with the C-terminal signal sequence of capsid protein in the BHK-21 cells using the pcDNA3.1 + mammalian expression vector. The immune assays performed demonstrated its immune reactivity equivalent to the parental JEV strain. Simultaneously performed ELISAs using the whole virus antigen and newly developed antigen gave comparable results for JE positive and negative samples, which established the utility of developed JEV E-VLP as an antigen. Reduced cross-reactivity and increased specificity were observed when tested with dual positive sera for anti-JEV and DENV antibodies. These findings confirm the efficiency and reliability of newly developed recombinant E-VLP antigen expressed by the BHK-IE6 cell clone as an antigen in serodiagnostic assays. The implementation and progress in developing cross-reactivity-reduced antigens would improve serodiagnosis and disease burden estimates of flavivirus infection.
Key points
• pcDNA3.1/JE-Sig-prM-E plasmid transfected BHK-21 cells stably express VLPs.
• Sodium butyrate induction enhanced the extracellular expression of VLPs.
• Application of JEV-E VLPs increases the specificity of JE IgM ELISA.
Journal Article
Synthesis, characterization, computational and biological evaluation of pyrazole hydrazones as promising anti-inflammatory agents
2025
In this study, two pyrazole-based hydrazone derivatives, 5-methyl-1-phenyl-4-(1-(2-phenylhydrazineylidene)ethyl)-1
H
-pyrazole (
PMPH
) and 1-(4-fluorophenyl)-5-methyl-4-(1-(2-phenylhydrazineylidene)ethyl)-1
H
-pyrazole (
4
F
-
PMPH
), were synthesized and the structures of the compounds were elucidated through FT-IR,
1
H and
13
C NMR, and mass spectral methods. The anti-inflammatory potential was evaluated using the bovine serum albumin denaturation assay, with
PMPH
and
4
F-PMPH
showing maximum inhibition at 0.5 mg/mL, respectively, suggesting that fluorine substitution enhances bioactivity. Molecular docking studies against COX-II (PDB: 3LN1) revealed favorable binding energies of − 7.21 kcal/mol (
PMPH
) and − 8.03 kcal/mol (
4
F-PMPH
). Molecular dynamics simulation of the best docked compound
4
F-PMPH
with COX-II (PDB: 3LN1) revealed a stable complex over a 100 ns simulation, supporting its potential as a promising inhibitor. In silico ADME analyses revealed pharmacokinetic behavior and drug-likeness. A comparative Density functional theory-based spectroscopic and electronic investigation was conducted using the B3LYP/6-31G(d,p) level of theory. Vibrational frequency analysis showed strong correlation between theoretical and experimental IR spectra. Frontier molecular orbital analysis, molecular electrostatic surface potential maps, Mulliken charges, electronic and global reactivity parameters were also studied. Besides, reduced density gradient, non-covalent interaction, electron localization function, and localized orbital locator maps were analyzed for both the compounds.
Journal Article
Design, synthesis, and computational insights into 3-acetyl-8-methoxy coumarin hybrids as potential anti-alzheimer’s agents
2025
The most prevalent degenerative brain disease, Alzheimer’s disease (AD), is characterized by cognitive function impairment. The ability to code new memories is lost in AD patients, and their lives are very challenging. Inhibitors of cholinesterase (ChE) and monoamine oxidase (MAO) have drawn interest as potential therapies for AD. To combat Alzheimer’s disease (AD), a new class of Coumarin-hydrazone hybrids has been synthesized
3(a-m).
Compounds
3a
,
3e
, and
3l
exhibited significant acetylcholinesterase (AChE) inhibitory activity with low IC
50
values of 7.40 ± 0.14 µM, 8.01 ± 0.70 µM, and 8.54 ± 1.01 µM, respectively. Additionally, these compounds, along with
3k
, demonstrated potent butyrylcholinesterase (BChE) inhibition, with IC
50
values from 65.41 ± 4.55 µM to 74.98 ± 5.30 µM, highlighting their dual cholinesterase inhibitory potential. Compound like
3a
(1.44 ± 0.03 µM),
3e
(1.51 ± 0.13 µM), and
3l
(1.65 ± 0.03 µM) display robust MAO-A inhibition, suggesting high potency. To see how the most potent inhibitor chemicals affected the substrate–enzyme relationship, enzyme kinetic tests were conducted in addition to enzyme inhibition investigations. Compound
3e
may function as a dual binding site AChE inhibitor, according to docking studies in addition to in vitro testing.
Journal Article