Molecular Modeling Studies Research Articles

Synthesis, structural investigations, in vitro cytotoxicity, apoptotic activity, cell cycle analysis, and molecular modeling studies of nano‐sized Zn(II) Schiff base complex

A new novel tetradentate ligand, [(1E,1′E)‐N,N′‐(1,2‐phenylene)bis(1‐(5‐(2‐fluorophenyl)furan‐2‐yl)methanimine) (PFPFMI), and its nano‐sized [Zn(PFPFMI)Cl2].3H2O complex were synthesized. The geometry of PFPFMI and its Zn(II) complex was described through CHN analyses, Fourier‐transform infrared spectroscopy (FTIR), UV–visible, X‐ray diffraction (XRD), thermal gravimetric analysis (TGA), and mass spectral data tests. The spectral data of the nano‐sized [Zn(PFPFMI)Cl2].3H2O complex indicates that the PFPFMI ligand functions as a tetradentate (N2O2) coordination through two azomethine nitrogen groups (N) and two furan ring oxygen (O) atoms. Density functional theory (DFT) calculations were performed using the molecular studio software to investigate the optimal geometry of PFPFMI and its [Zn(PFPFMI)Cl2].3H2O complex. The SEM, TEM, XRD, AFM, and energy dispersive X‐ray analysis (EDX) analyses of the studied complex unveil distinct and strong diffraction peaks, indicating its crystalline nature and providing evidence of its nano‐sized particle sizes. Additionally, the inhibition zone diameter was used to assess the in vitro antimicrobial action of PFPFMI and the particular complex against Gram‐positive bacteria Streptococcus pneumonia and Bacillus subtilis, Gram‐negative bacteria Pseudomonas aeruginosa, Salmonella typhi, and Escherichia coli, as well as fungi Aspergillus fumigatus, Geotricum candidum, Syncephalastrum racemosum, and Candida tropicalis. The [Zn(PFPFMI)Cl2].3H2O complex exhibits higher activity than the ligand PFPFMI. In vitro cytotoxicity of the synthesized [Zn(PFPFMI)Cl2].3H2O complex was explored using MCF7 (breast cancer), HCT116 (colon cancer), A549 (lung cancer), HePG‐2 (liver cancer), A375 (melanoma cancer), and normal lung fibroblast (WI38) cell lines. Based on IC50 and selective index (SI) values, it was shown that the complex exhibited higher potency against MCF7 cell lines. Moreover, the Zn(II) complex exhibited the ability to induce DNA damage in MCF7 cells, resulting in dose‐dependent cell apoptosis. Subsequent investigations revealed that complex 2 also induced cell cycle arrest in the G2 and S phases.

Regiodivergent biosynthesis of bridged bicyclononanes

Medicinal compounds from plants include bicyclo[3.3.1]nonane derivatives, the majority of which are polycyclic polyprenylated acylphloroglucinols (PPAPs). Prototype molecules are hyperforin, the antidepressant constituent of St. John’s wort, and garcinol, a potential anticancer compound. Their complex structures have inspired innovative chemical syntheses, however, their biosynthesis in plants is still enigmatic. PPAPs are divided into two subclasses, named type A and B. Here we identify both types in Hypericum sampsonii plants and isolate two enzymes that regiodivergently convert a common precursor to pivotal type A and B products. Molecular modelling and substrate docking studies reveal inverted substrate binding modes in the two active site cavities. We identify amino acids that stabilize these alternative binding scenarios and use reciprocal mutagenesis to interconvert the enzymatic activities. Our studies elucidate the unique biochemistry that yields type A and B bicyclo[3.3.1]nonane cores in plants, thereby providing key building blocks for biotechnological efforts to sustainably produce these complex compounds for preclinical development.

In vitro anti-microbial, DNA-binding, In silico pharmacokinetics and molecular docking studies of Schiff-based Cu(II), Zn(II) and Pd(II) complexes

Synthesis of salen type Schiff base ligand by the condensation of butane 1,4-diamine with 5-bromosalicyaldehyde has been done. Further, three new mononuclear Schiff based complexes of Cu(II), Zn(II) and Pd(II) have been prepared by the reaction of the Schiff base ligand with appropriate metal salts. The developed Schiff base ligand and metal complexes of Cu(II), Zn(II) and Pd(II) have been well characterized by various spectroscopic techniques like UV–Vis, FT-IR, 1H-NMR, 13C-NMR, EPR, Mass and powder XRD. All the synthesized Schiff base compounds have been tested for antibacterial, antifungal, hemolysis assay and DNA binding activities. The zone inhibition measurements revealed the supremacy and enhanced efficiency of metal complexes as compared to free ligand. The molecular modelling studies were carried to analyze the bonding affinity and inhibition probability of the synthesized complexes with the S. aureus nucleoside diphosphate kinase receptor. The in-silico pharmacokinetics studies such as Lipinski's rule, Veber's rule, drug-likeness score and physiochemical parameters analysis predicted the drug-likeness of the synthesized compounds.

Retraction: Spectroscopic and molecular modeling studies of binding interaction between the new complex of yttrium and 1,10-phenanthroline derivatives with DNA and BSA.

[This retracts the article DOI: 10.3389/fchem.2023.1231504.].

Synthesis and molecular modeling study of new pyrimidine-based derivatives as anticonvulsant agents

Synthesis and molecular modeling study of new pyrimidine-based derivatives as anticonvulsant agents

The Suppressive Effect of Novel Hydrazones‐Tethered Imidazoles in HCT‐116 and HT‐29 Colorectal Cancer Cells: Synthesis, Biological Activity and Molecular Modeling Studies

AbstractA series of hybrid compounds containing both the imidazole ring and the hydrazone moiety have been synthesized. Synthesized compounds were characterized by various spectral techniques, including FT‐IR, 1H‐NMR, 13C‐NMR, and HRMS. The compounds were evaluated for their antiproliferative activities on colorectal cancer cells HCT‐116 and HT‐29 in a time‐dependent manner. Among them, some compounds exhibited remarkable anti‐cancer activity with a less cytotoxic effect on non‐cancerous cell lines, especially HRK‐2 with IC50 value of 1.35±0.18 μM in HCT‐116 cells and HRK‐5 with IC50 value of 2.67±0.61 μM in HT‐29 cells. Investigations of colon cancer cell death were performed, and the most active compounds were found to trigger cell death via nuclear localization and induce S phase arrest of the colon cancer cell. Moreover, molecular modeling studies for the synthesized compounds was performed to predict their binding affinities toward the active site of BCL‐2. The findings of the molecular modeling investigations were highly consistent with those of the cytotoxicity results.

Molecular insights into the antioxidant and anticancer properties: A comprehensive analysis through molecular modeling, docking, and dynamics studies.

Plants are rich sources of therapeutic compounds that often lack the side effects commonly found in synthetic chemicals. Researchers have effectively synthesized pharmaceuticals from natural sources, taking inspiration from traditional medicine, in their pursuit of modern drugs. This study aims to evaluate the phenolic and flavonoid content of Solanum virginianum seeds using different solvent extracts, enzymatic assays including 2,2-diphenyl-1-picrylhydrazylactivity, reducing power, and superoxide activity. Our phytochemical screening identified active compounds, such as phenols, flavonoids, tannins, and alkaloids. The methanol extract notably possesses higher levels of total phenolic and flavonoid content in comparison to the other extracts. The results highlight the superior antioxidant activity of methanol-extracted leaves, demonstrated by their exceptional IC50 values, which surpass the established standard. In this study, molecular docking techniques were used to assess the binding affinity and to predict the binding conformation of the compounds. Quercetin 3-O beta-d-galactopyranoside displayed a binding energy of -8.35 kcal/mol with several important amino acid residues, PHE222, TRP440, ILE184, LEU192, VAL221, LEU218, SER185, and ALA188. Kaempferol 3-O-beta-l-glucopyranoside exhibited a binding energy of -8.33 kcal/mol, interacting with specific amino acid residues including ALA 441, VAL318, VAL322, MET307, ILI409, GLY442, and PHE439. The results indicate that the methanol extract has a distinct composition of biologically active constituents compared to the other extracts. Overall, seeds exhibit promise as natural antioxidants and potential agents for combating cancer. This study highlights the significance of utilizing the therapeutic capabilities of natural compounds and enhancing our comprehension of their pharmacological characteristics.

Investigating the Taenia solium Fatty Acid Binding Protein Superfamily for Their Immunological Outlook and Prospect for Therapeutic Targets.

Taenia solium, like other helminthic parasites, lacks key components of cellular machinery required for endogenous lipid biosynthesis. This deficiency compels the parasite to obtain all of its lipid requirements from its host. The passage of lipids across the cell membrane is tightly regulated. To facilitate effective lipid transport, the cestode parasite utilizes certain lipid binding proteins called FABPs. These FABPs bind with the lipid ligands and allow the transport of lipids across the membranes and into the cytosol. Here, by integrating a computational with homology protein prediction tools, we had identified five FABPs in the T. solium proteome. We confirmed their presence by RNA expression analysis of respective genes from the parasite's cysticerci transcript. During the molecular modeling and MD simulation studies, two of them, TsM_000544100 and TsM_001185100, were most stable. Furthermore, they had a robust interaction with the IgG1 molecule, as evidenced by MD simulation. In addition, by employing in silico screening, we had identified potential ligand interacting residues that are present on the probable druggable site. In combination with in vitro cysticidal assays, enalaprilat dihydrate showed efficacy against cysticerci, which suggests that FABPs play a significant role in the cysticercus life cycle. Together, we provided a detailed distribution of all FABPs expressed by T. solium cysticerci and the critical role of TsM_001185100 in cysticercus viability.

Aminocarbonylation of 2-(N-substituted) 5-iodobenzoates: synthesis of glyoxylamido-anthranilates, their cytotoxicity and molecular modeling study

Aminocarbonylation of 2-(N-substituted) 5-iodobenzoates: synthesis of glyoxylamido-anthranilates, their cytotoxicity and molecular modeling study

CCL18 aggravates atherosclerosis by inducing CCR6-dependent T-cell influx and polarization.

The CC chemokine ligand 18 (CCL18) is a chemokine highly expressed in chronic inflammation in humans. Recent observations of elevated CCL18 plasma levels in patients with acute cardiovascular syndromes prompted an investigation into the role of CCL18 in the pathogenesis of human and mouse atherosclerosis. CCL18 was profoundly upregulated in ruptured human atherosclerotic plaque, particularly within macrophages. Repeated administration of CCL18 in Western-type diet-fed ApoE -/- mice or PCSK9mut-overexpressing wild type (WT) mice led to increased plaque burden, enriched in CD3+ T cells. In subsequent experimental and molecular modeling studies, we identified CCR6 as a functional receptor mediating CCL18 chemotaxis, intracellular Ca2+ flux, and downstream signaling in human Jurkat and mouse T cells. CCL18 failed to induce these effects in vitro in murine spleen T cells with CCR6 deficiency. The ability of CCR6 to act as CCL18 receptor was confirmed in vivo in an inflammation model, where subcutaneous CCL18 injection induced profound focal skin inflammation in WT but not in CCR6-/- mice. This inflammation featured edema and marked infiltration of various leukocyte subsets, including T cells with a Th17 signature, supporting CCR6's role as a Th17 chemotactic receptor. Notably, focal overexpression of CCL18 in plaques was associated with an increased presence of CCR6+ (T) cells. Our studies are the first to identify the CCL18/CCR6 axis as a regulator of immune responses in advanced murine and human atherosclerosis.

Benzamide Trimethoprim Derivatives as Human Dihydrofolate Reductase Inhibitors-Molecular Modeling and In Vitro Activity Study.

Human dihydrofolate reductase (hDHFR) is an essential cellular enzyme, and inhibiting its activity is a promising strategy for cancer therapy. We have chosen the trimethoprim molecule (TMP) as a model compound in our search for a new class of hDHFR inhibitors. We incorporated an amide bond, a structural element typical of netropsin, a ligand that binds selectively in the minor groove of DNA, into the molecules of TMP analogs. In this work, we present previously obtained and evaluated eleven benzamides (JW1-JW8; MB1, MB3, MB4). Recently, these compounds were specifically projected as potential inhibitors of the enzymes acetylcholinesterase (AChE) and β-secretase (BACE1). JW8 was most active against AChE, with an inhibitory concentration of AChE IC50 = 0.056 µM, while the IC50 for donepezil was 0.046 µM. This compound was also the most active against the BACE1 enzyme. The IC50 value was 9.01 µM compared to that for quercetin, with IC50 = 4.89 µM. All the benzamides were active against hDHFR, with IC50 values ranging from 4.72 to 20.17 µM, and showed activity greater than TMP (55.26 µM). Quantitative results identified the derivatives JW2 and JW8 as the most promising. A molecular modeling study demonstrates that JW2 interacts strongly with the key residue Gly-117, while JW8 interacts strongly with Asn-64 and Arg-70. Furthermore, JW2 and JW8 demonstrate the ability to stabilize the hDHFR enzyme, despite forming fewer hydrogen bonds with the protein compared to reference ligands. It can be concluded that this class of compounds certainly holds great promise for good active leads in medicinal chemistry.

Stimulus-Induced Dynamic Behavior Regulation of Flexible Crystals through the Tuning of Module Rigidity.

Introducing dynamic behavior into periodic frameworks has borne fruit in the form of flexible porous crystals. The detailed molecular design of frameworks in order to control their collective dynamics is of particular interest, for example, to achieve stimulus-induced behavior. Herein, by varying the degree of rigidity of ditopic pillar linkers, two isostructural flexible metal-organic frameworks (MOFs) with common rigid supermolecular building bilayers were constructed. The subtle substitution of single (in bibenzyl-4,4'-dicarboxylic acid; H2BBDC) with double (in 4,4'-stilbenedicarboxylic acid; H2SDC) C-C bonds in pillared linkers led to markedly different flexible behavior of these two MOFs. Upon the removal of guest molecules, both frameworks clearly show reversible single-crystal-to-single-crystal transformations involving the cis-trans conformation change and a resulting swing of the corresponding pillar linkers, which gives rise to Flex-Cd-MOF-1a and Flex-Cd-MOF-2a, respectively. Strikingly, a more favorable gas-induced dynamic behavior in Flex-Cd-MOF-2a was verified in detail by stepwise C3H6/C3H8 sorption isotherms and the corresponding in situ powder X-ray diffraction experiments. These insights are strongly supported by molecular modeling studies on the sorption mechanism that explores the sorption landscape. Furthermore, a consistency between the macroscopic elasticity and microscopic flexibility of Flex-Cd-MOF-2 was observed. This work fuels a growing interest in developing MOFs with desired chemomechanical functions and presents detailed insights into the origins of flexible MOFs.

Spectroscopic, biochemical and computational studies of bioactive DNA minor groove binders targeting 5′-WGWWCW-3′ motif

Spectroscopic, biochemical, and computational modelling studies have been used to assess the binding capability of a set of minor groove binding (MGB) ligands against the self-complementary DNA sequences 5′-d(CGCACTAGTGCG)-3′ and 5′-d(CGCAGTACTGCG)-3′. The ligands were carefully designed to target the DNA response element, 5′-WGWWCW-3′, the binding site for several nuclear receptors. Basic 1D 1H NMR spectra of the DNA samples prepared with three MGB ligands show subtle variations suggestive of how each ligand associates with the double helical structure of both DNA sequences. The variations among the investigated ligands were reflected in the line shape and intensity of 1D 1H and 31P-{1H} NMR spectra. Rapid visual inspection of these 1D NMR spectra proves to be beneficial in providing valuable insights on MGB binding molecules. The NMR results were consistent with the findings from both UV DNA denaturation and molecular modelling studies. Both the NMR spectroscopic and computational analyses indicate that the investigated ligands bind to the minor grooves as antiparallel side-by-side dimers in a head-to-tail fashion. Moreover, comparisons with results from biochemical studies offered valuable insights into the mechanism of action, and antitumor activity of MGBs in relation to their structures, essential pre-requisites for future optimization of MGBs as therapeutic agents.

Synthesis of novel indol-3-acetamido analogues as potent anticancer agents, biological evaluation and molecular modeling studies

Cannabinoids bind to cannabinoid receptors CB1 and CB2 and their antitumoral activity has been reported against some various cancer cell lines. Some synthetic cannabinoids possessing indole rings such as JWH-015 and JWH-133 particularly bind to the cannabinoid CB2 receptor and it was reported that they inhibit the proliferation and growth of various cancer cells without their psychoactive effects. However, the pharmacological action mechanisms of the cannabinoids are completely unknown. In this study, we report the synthesis of some new cannabinoidic novel indoles and evaluate their anticancer activity on various cancerous and normal cell lines (U87, RPMI 8226, HL60 and L929) using several cellular and molecular assays including MTT assay, real-time q-PCR, scratch assay, DAPI assay, Annexin V-PE/7AAD staining, caspase3/7 activity tests. Our findings indicated that compounds 7, 10, 13, 16, and 17 could reduce cell viability effectively. Compound 17 markedly increased proapoptotic genes (BAX, BAD, and BIM), tumor suppressor gene (p53) expression levels as well as the BAX/BCL-2 ratio in U87 cells. In addition, 17 inhibited cell migration. Based on these results, 17 was chosen for determining the mechanism of cell death in U87 cells. DAPI and Annexin V-7AAD staining results showed that 17 induced apoptosis, moreover activated caspase 3/7 significantly. Hence, compound 17, was selected as a lead compound for further pharmacomodulation. To rationalize the observed biological activities of 17, our study also included a comprehensive analysis using molecular docking and MD simulations. This integrative approach revealed that 17 fits tightly into the active site of the CB2 receptor and is involved in key interactions that may be responsible for its anti-proliferative effects.

New-generation biofilm effective antimicrobial peptides and a real-time anti-biofilm activity assay: CoMIC

Nowadays, it is very important to produce new-generation drugs with antimicrobial properties that will target biofilm-induced infections. The first target for combating these microorganisms, which are the source itself. Antimicrobial peptides, which are more effective than antibiotics due to their ability to kill microorganisms and use a different metabolic pathway, are among the new options today. The aim of this study is to develop new-generation antibiotics that inhibit both biofilm-producing bacteria and the biofilm itself. For this purpose, we designed four different peptides by combining two amino acid forms (D- and L-) with the same sequence having alpha helix structures. It was found that the combined use of these two forms can increase antimicrobial efficacy more than 30-fold. These results are supported by molecular modeling and scanning electron microscopy (SEM), at the same time cytotoxicity (IC50) and hemotoxicity (HC50) values remained within the safe range. Furthermore, antibiofilm activities of these peptides were investigated. Since the existing biofilm inhibition methods in the literature do not technically simulate the exact situation, in this study, we have developed a real-time observable biofilm model and a new detection method based on it, which we call the CoMIC method. Findings have shown that the NET1 peptide with D-leucine amino acid in its structure and the NET3 peptide with D-arginine amino acid in its structure are effective in inhibiting biofilm. As a conclusion, our peptides can be considered as potential next-generation broad-spectrum antibiotic molecule/drug candidates that might be used in biofilm and clinical important bacteria.Key points• Antimicrobial peptides were developed to inhibit both biofilms producing bacteria and the biofilm itself.• CoMIC will fill a very crucial gap in understanding biofilms and conducting the necessary quantitative studies.• Molecular modelling studies, NET1 peptide molecules tends to move towards and adhere to the membrane within nanoseconds.

Isolation and characterization of thymoquinone from Nigella sativa essential oil: antioxidant and antibacterial activities, molecular modeling studies, and cytotoxic effects on lung cancer A549 cells

Thymoquinone (TQ), a bioactive compound found in Nigella sativa seeds, has gained considerable attention due to its potential therapeutic properties. This study aimed to isolate and characterize TQ from Nigella sativa essential oil and evaluate its antioxidant capacity, antibacterial activity, and cytotoxic effects on lung cancer A549 cells. Moreover, The binding potential of TQ to Keap1 (Kelch-like ECH associated protein 1) was investigated through molecular docking. The stability of the resulting complex was evaluated through molecular dynamics (MD) simulation. The CUPRAC assay revealed significant antioxidant capacity of TQ, as indicated by its high molar absorptivity coefficient. TQ also demonstrated notable free radical scavenging activity, with efficacy increasing with concentration. In terms of antiquorum sensing activity, TQ displayed effectiveness against all tested virulence factors in P. aeruginosa PAO1 and Chromobacterium violaceum in different range. Additionally, TQ induced cytotoxicity in non-small lung cancer cells, inhibiting cell viability. In conclusion, this study successfully isolated and characterized TQ from Nigella sativa seeds and demonstrated its remarkable antioxidant capacity, antibacterial activity, and cytotoxic effects on lung cancer cells. These findings suggest the potential of TQ for various applications in the food and pharmaceutical industries. The wet-lab study demonstrated that TQ had an antioxidant effect. The TQ was found to have high binding potential to Keap1 as it formed four conventional hydrogen bonds with the protein. The resulting Keap1-TQ complex was also found to be stable. Further research is warranted to explore the therapeutic potential of TQ and develop novel treatments based on its properties.

Chemical composition of leaf essential oil of Schinopsis lorentzii and its inhibitory effects against key enzymes relevant to type-2 diabetes: an emphasis on GC-MS chemical profiling and molecular docking studies

Schinopsis lorentzii (Griseb.) Engler is an aromatic plant belonging to Anacardiaceae family, and grown in Argentina, Paraguay, Brazil, and Bolivia. It is a rich source of essential oils and tannins as well as commercially available as vegetable-processed leather tanning and antiparasitic agent. This study was designed to explore the chemical composition of essential oil isolated from S. lorentzii leaves and elaborate on their significance as natural anti-diabetic, combined with molecular-docking studies. The leaf oil was chemically analysed using gas chromatography-mass spectrometry (GC-MS) method and investigated for inhibitory effects against α-amylase and α-glucosidase. Molecular-modelling study via Molecular Operating Environment-Docking (MOE-Dock) program was used to evaluate binding interactions of major components with the above-mentioned targets. The GC-MS analysis of the leaf oil revealed the predominance of β-caryophyllene (21.63±0.36%), γ-terpinene (13.53±0.74%), α-pinene (13.38±0.65%), and terpinen-4-ol (12.55±1.56%). The tested oil expressed a remarkable inhibitory effect against α-amylase with IC50 value of 2.27±0.19 μg/mL, comparable to acarbose (IC50 = 0.52±0.18 μg/mL) used as standard drug. Similarly, it significantly inhibited α-glucosidase (IC50 = 0.84±0.03 μg/mL), compared to acarbose (IC50 = 0.38±0.02μg/mL). The in-silico molecular docking study revealed favorable binding affinities of β-caryophyllene, terpinen-4-ol and sabinene with variable degrees with α-amylase and α-glucosidase. Thus, this study demonstrated valuable scientific data on the leaf oil of S. lorentzii as a potential candidate for the development of natural antidiabetic formulations.

Kinetics and molecular modeling studies on the inhibition mechanism of GH13 α-glycosidases by small molecule ligands

Alpha-glucosidase inhibitors play an important role in Diabetes Mellitus (DM) treatment since they prevent postprandial hyperglycemia. The Glycoside Hydrolase family 13 (GH13) is the major family of enzymes acting on substrates containing α-glucoside linkages, such as maltose and amylose/amylopectin chains in starch. Previously, our group identified glycoconjugate 1H-1,2,3-triazoles (GCTs) inhibiting two GH13 α-glycosidases: yeast maltase (MAL12) and porcine pancreatic amylase (PPA). Here, we combined kinetic studies and computational methods on nine GCTs to characterize their inhibitory mechanism. They all behaved as reversible inhibitors, and kinetic models encompassed noncompetitive and various mechanisms of mixed-type inhibition for both enzymes. Most potent inhibitors displayed Ki values of 30 μM for MAL12 (GPESB16) and 37 μM for PPA (GPESB15). Molecular dynamics and docking simulations indicated that on MAL12, GPESB15 and GPESB16 bind in a cavity adjacent to the active site, while on the PPA, GPESB15 was predicted to bind at the entrance of the catalytic site. Notably, despite its putative location within the active site, the binding of GPESB15 does not obstruct the substrate's access to the cleavage site. Our study contributes to paving the way for developing novel therapeutic strategies for managing DM-2 through GH13 α-glycosidases inhibition.

Experiments and Molecular Simulations to Study the Effect of Surface-Active Compounds in Mixtures of Model Oils on CO2 Corrosion during Intermittent Oil-Water Wetting.

Intermittent oil-water wetting can have a significant effect on the internal corrosion of steel pipelines. This paper presents a combined experimental and molecular modeling study of several influential factors on the surface properties and corrosion behavior of mild steel in CO2 environments. The influence of different model oils (LVT-200 and Aromatic-200) and select surface-active compounds (myristic acid, cyclohexane butyric acid, and oleic acid) on the corrosion behavior of carbon steel during intermittent oil-water wetting was determined by measuring the corrosion rate after intermittent wetting cycles. The interfacial tension measurements were performed to study the incorporation of the oil phase along with surface-active molecules in the protective layer formed on the specimen surface. Results showed that the interfacial tension for an aromatic oil-water interface is lower than that for an aliphatic oil-water interface. To understand this result, molecular dynamics simulations of oil-water interfaces were performed in the presence of surface-active molecules and different oils to analyze the structure of the layer formed at the interface. The simulations supported the hypothesis that aromatic molecules are less structured at the interface, which results in the incorporation of more water molecules into the protective layer formed at the steel surface, causing a higher corrosion rate. On the other hand, the simulations revealed that myristic acid in an aliphatic oil forms a well-aligned structure at the interface, devoid of any water molecules. This is in agreement with the hypothesis that the linear molecular structure of myristic acid favors the alignment of molecules at an aliphatic oil-water interface, resulting in a lower interfacial tension and more effective corrosion mitigation as compared to the other two nonlinear compounds tested. It is concluded that an important factor controlling the corrosion behavior is the molecular structure of the oil-water interface, which is adopted by the steel surface layer through the Langmuir-Blodgett process.

Exploring different classification-dependent QSAR modelling strategies for HDAC3 inhibitors in search of meaningful structural contributors.

Histone deacetylase 3 (HDAC3), a Zn2+-dependent class I HDACs, contributes to numerous disorders such as neurodegenerative disorders, diabetes, cardiovascular disease, kidney disease and several types of cancers. Therefore, the development of novel and selective HDAC3 inhibitors might be promising to combat such diseases. Here, different classification-based molecular modelling studies such as Bayesian classification, recursive partitioning (RP), SARpy and linear discriminant analysis (LDA) were conducted on a set of HDAC3 inhibitors to pinpoint essential structural requirements contributing to HDAC3 inhibition followed by molecular docking study and molecular dynamics (MD) simulation analyses. The current study revealed the importance of hydroxamate function for Zn2+ chelation as well as hydrogen bonding interaction with Tyr298 residue. The importance of hydroxamate function for higher HDAC3 inhibition was noticed in the case of Bayesian classification, recursive partitioning and SARpy models. Also, the importance of substituted thiazole ring was revealed, whereas the presence of linear alkyl groups with carboxylic acid function, any type of ester function, benzodiazepine moiety and methoxy group in the molecular structure can be detrimental to HDAC3 inhibition. Therefore, this study can aid in the design and discovery of effective novel HDAC3 inhibitors in the future.