Prediction of Properties from Simulations: Free Energies of Solvation in Hexadecane, Octanol, and Water

Unraveling the molecular basis for effective regulation of integrin α5β1 for enhanced therapeutic interventions

Cell attachment to the extracellular matrix significantly impacts the integrity of tissues and human health. The integrin α5β1 is a heterodimer of α5 and β1 subunits and has been identified as a crucial modulator in several human carcinomas. Integrin α5β1 significantly regulates cell proliferation, angiogenesis, inflammation, tumor metastasis, and invasion. This regulatory role of integrin α5β1 in tumor metastasis makes it an appealing target for cancer therapy. The majority of the drugs targeting integrin α5β1 are limited only to clinical trials. In our study, we have performed 94287 compounds screening to determine potential drugs against α5β1 integrin. We have used ATN-161 as a reference and employed combined bioinformatic methodologies, including molecular modelling, virtual screening, MM-GBSA, cell-line cytotoxicity prediction, ADMET, Density Functional Theory (DFT), Non-covalent Interactions (NCI) and molecular simulation, to identify putative integrin α5β1 inhibitors. We found Taxifolin, PD133053, and Acebutolol that possess inhibitory activity against α5β1 integrin and could act as effective drug for the cancer treatment. Taxifolin, PD133053, and Acebutolol exhibited excellent binding to the druggable pocket of integrin α5β1, and also maintained a unique binding mechanism with extra hydrophobic contacts at molecular level. Overall, our study gives new pharmacological candidates that may act as a potential drug against integrin α5β1.

Dynamics of small molecule-enzyme interactions: Novel benzenesulfonamides as multi-target agents endowed with inhibitory effects against some metabolic enzymes

In contemporary medicinal chemistry, employing a singular small molecule to concurrently multi-target disparate molecular entities is emerging as a potent strategy in the ongoing battle against metabolic disease. In this study, we present the meticulous design, synthesis, and comprehensive biological evaluation of a novel series of 1,2,3-triazolylmethylthio-1,3,4-oxadiazolylbenzenesulfonamide derivatives (8a-m) as potential multi-target inhibitors against human carbonic anhydrase (EC.4.2.1.1, hCA I/II), α-glycosidase (EC.3.2.1.20, α-GLY), and α-amylase (EC.3.2.1.1, α-AMY). Each synthesized sulfonamide underwent rigorous assessment for inhibitory effects against four distinct enzymes, revealing varying degrees of hCA I/II, a-GLY, and a-AMY inhibition across the tested compounds. hCA I was notably susceptible to inhibition by all compounds, demonstrating remarkably low inhibition constants (KI) ranging from 42.20 ± 3.90 nM to 217.90 ± 11.81 nM compared to the reference standard AAZ (KI of 439.17 ± 9.30 nM). The evaluation against hCA II showed that most of the synthesized compounds exhibited potent inhibition effects with KI values spanning the nanomolar range 16.44 ± 1.53-70.82 ± 4.51 nM, while three specific compounds, namely 8a-b and 8d, showcased lower inhibitory potency than other derivatives that did not exceed that of the reference drug AAZ (with a KI of 98.28 ± 1.69 nM). Moreover, across the spectrum of synthesized compounds, potent inhibition profiles were observed against diabetes mellitus-associated α-GLY (KI values spanning from 0.54 ± 0.06 μM to 5.48 ± 0.50 μM), while significant inhibition effects were noted against α-AMY, with IC50 values ranging between 0.16 ± 0.04 μM and 7.81 ± 0.51 μM) compared to reference standard ACR (KI of 23.53 ± 2.72 μM and IC50 of 48.17 ± 2.34 μM, respectively). Subsequently, these inhibitors were evaluated for their DPPH· and ABTS+· radical scavenging activity. Moreover, molecular docking investigations were meticulously conducted within the active sites of hCA I/II, α-GLY, and α-AMY to provide comprehensive elucidation and rationale for the observed inhibitory outcomes.

Discovery of New Highly Potent Histamine H3 Receptor Antagonists, Calcium Channel Blockers, and Acetylcholinesterase Inhibitors

At present, one of the most promising strategies to tackle the complex challenges posed by Alzheimer's disease (AD) involves the development of novel multitarget-directed ligands (MTDLs). To this end, we designed and synthesized nine new MTDLs using a straightforward and cost-efficient one-pot Biginelli three-component reaction. Among these newly developed compounds, one particular small molecule, named 3e has emerged as a promising MTDL. This compound effectively targets critical biological factors associated with AD, including the simultaneous inhibition of cholinesterases (ChEs), selective antagonism of H3 receptors, and blocking voltage-gated calcium channels. Additionally, compound 3e exhibited remarkable neuroprotective activity against H2O2 and Aβ1-40, and effectively restored cognitive function in AD mice treated with scopolamine in the novel object recognition task, confirming that this compound could provide a novel and innovative therapeutic approach for the effective treatment of AD.

Synthesis and Characterization of Folic Acid-Conjugated Terbium Complexes as Luminescent Probes for Targeting Folate Receptor-Expressing Cells

Several conjugates between folic acid and a series of kinetically stable lanthanide complexes have been synthesized, using amide coupling and azide-alkyne cycloaddition methodologies to link the metal-binding domain to folate through a variety of spacer groups. While all these complexes exhibit affinity for the folate receptor, it is clear that the point of attachment to folate is essential, with linkage through the γ-carboxylic acid giving rise to significantly enhanced receptor affinity. All the conjugates studied show affinities consistent with displacing biological circulating folate derivatives, 5-methyltetrahydrofolate, from folate receptors. All the complexes exhibit luminescence with a short-lived component arising from ligand fluorescence overlaid on a much longer lived terbium-centered component. These can be separated using time-gating methods. From the results obtained, the most promising approach to achieve sensitized luminescence in these systems requires incorporating a sensitizing chromophore close to the lanthanide.

Effect of ion to ligand ratio on the aqueous to organic relative solubility of a lanthanide-ligand complex

In the solvent extraction of rare earth elements, mechanistic aspects remain unclear regarding where and how extractant molecules coordinate metal ions and transport them from the aqueous phase into the organic phase. Molecular dynamics simulations were used to examine how unprotonated di(2-ethylhexyl)phosphoric acid (DEHP-) ligands that coordinate the Gd3+ ion can transfer the ion across the water-organic interface. Using the umbrella sampling technique, potential of mean force profiles were constructed to quantify the relative solubility of the Gd3+ ion coordinated to 0-3 DEHP- ligands in either water, 1-octanol, or hexane solvents and at the water-organic interfaces. The simulations show the Gd-DEHP- complexes, at varying Ln-ligand ratios, preferentially solvate on water-organic interfaces. While the Gd(DEHP-)3 complex will diffuse past the aqueous-organic interface into the octanol solvent, it is thermodynamically preferred for the Gd(DEHP-)3 complex to remain in the water-hexane interface when there is no amphiphilic layer of excess ligand.

Novel beta-lactam substituted benzenesulfonamides: in vitro enzyme inhibition, cytotoxic activity and in silico interactions

In this study, a library of twelve beta-lactam-substituted benzenesulfonamides (5a-l) was synthesized using the tail-approach method. The compounds were characterized using IR, 1H NMR, 13C NMR and elemental analysis techniques. These newly synthesized compounds were tested for their ability to inhibit the activity of two carbonic anhydrases (hCA) isoforms, I and II, and acetylcholinesterase (AChE) in vitro. The results showed that the synthesized compounds were potent inhibitors of hCA I, with KIs in the low nanomolar range (66.60-278.40 nM) than the reference drug acetazolamide (AAZ), which had a KI of 439.17 nM. The hCA II was potently inhibited by compounds 5a, 5d-g and 5l, with KIs of 69.56, 39.64, 79.63, 74.76, 78.93 and 74.94 nM, respectively (AAZ, KI of 98.28 nM). Notably, compound 5a selectively inhibited hCA II with a selectivity of > 4-fold over hCA I. In terms of inhibition of AChE, the synthesized compounds had KIs ranging from 30.95 to 154.50 nM, compared to the reference drug tacrine, which had a KI of 159.61 nM. Compounds 5f, 5h and 5l were also evaluated for their ability to inhibit the MCF-7 cancer cell line proliferation and were found to have promising anticancer activity, more potent than 5-fluorouracil and cisplatin. Molecular docking studies suggested that the sulfonamide moiety of these compounds fits snugly into the active sites of hCAs and interacts with the Zn2+ ion. Furthermore, molecular dynamics simulations were performed for 200 ns to assess the stability and dynamics of each enzyme-ligand complex. The acceptability of the compounds based on Lipinski's and Jorgensen's rules was also estimated from the ADME/T results. These results indicate that the synthesized molecules have the potential to be developed into effective and safe inhibitors of hCAs and AChE and could be lead agents.Communicated by Ramaswamy H. Sarma.

Isoreticular Curves: A Theory of Capillary Condensation To Model Water Sorption within Microporous Sorbents

Metal-organic frameworks have gained traction as leading materials for water sorption applications due to precise chemical tunability of their well-ordered pores. These applications include atmospheric water capture, heat pumps, desiccation, desalination, humidity control, and thermal batteries. However, the relationships between the framework pore structure and the measurable water sorption properties, namely critical relative humidity for condensation, maximal capacity, and pore size or temperature for the onset of hysteresis, have not been clearly delineated. Herein, we precisely formulate these relationships by application of the theory of capillary condensation and macroscopic thermodynamic models to a large data set of MOF water isotherms. These relationships include a concept termed isoreticular curves that relates the critical pressure for pore condensation (α), gravimetric capacity (Qmax), and hydrophilicity (the Gibbs free energy for binding water, ΔG) as Qmax = a1(ΔG/ln α)2 + a2(ΔG/ln α), with constants a1 and a2 dependent upon the density and volume occupied by the linker and secondary building unit, and framework topology. Through this analysis, we propose guidelines for the maximization of sorption capacity at a given relative humidity with minimal hysteresis and discuss the theoretical limits for capacity at low relative humidity. This model provides an explanation for the lack of high-capacity frameworks at low relative humidity, as increasing pore size also causes an increase in relative humidity. We propose a loose upper bound of Qmax = -0.25(1/ln α)2 - 1.75(1/ln α) for the limit of maximal capacity at a given relative humidity in the dry regime. These guidelines are consequential for the design of new materials for water sorption applications.

Fragment-based virtual screening identifies novel leads against Plasmepsin IX (PlmIX) of Plasmodium falciparum: Homology modeling, molecular docking, and simulation approaches

Despite continuous efforts to develop safer and efficient medications, malaria remains a major threat posing great challenges for new drug discovery. The emerging drug resistance, increased toxicities, and impoverished pharmacokinetic profiles exhibited by conventional drugs have hindered the search for new entities. Plasmepsins, a group of Plasmodium-specific, aspartic acid protease enzymes, are involved in many key aspects of parasite biology, and this makes them interesting targets for antimalarial chemotherapy. Among different isoforms, PlmIX serves as an unexplored antimalarial drug target that plays a crucial role along with PlmV and X in the parasite's survival by digesting hemoglobin in the host's erythrocytes. In this study, fragment-based virtual screening was performed by modeling the three-dimensional structure of PlmIX and predicting its ligand-binding pocket by using the Sitemap tool. Screening identified the fragments with the XP docking score ≤ -3 kcal/mol from the OTAVA General Fragment Library (≈16,397 fragments), and the selected fragments were chosen for ligand breeding. The resulting ligands (≈69,858 ligands) were subsequently subjected to filtering based on the QikProp properties along with carcinogenicity testing performed using CarcinoPred-EL and then docked in the SP (≈14,078 ligands) as well as XP mode (≈3,104 ligands), and compared with that of control ligands 49C and I0L. The top-ranked ligands were taken further for the calculation of the free energy of binding using Prime MM-GBSA. Overall, a total of six complexes were taken further for MD simulation studies performed at 100 ns to attain a better understanding of the binding mechanisms, and compounds 3 and 4 were found to be the most efficient ones in silico. The analysis of compound 3 revealed that the carbonyl group present in position 1 on the isoindoline moiety (Arg554) was responsible for inhibitory activity against PlmIX. However, the analysis of compound 4 revealed that the amide linkage sandwiched between the phenyl ring and isoquinoline moiety (Lys555 and Ser226) as well as carbonyl oxygen of the carbamoyl group present at position 2 of the pyrazole ring (Gln222) were responsible for PlmIX inhibitory activity, owing to their crucial interactions with key amino acid residues.

Novel spiroindoline derivatives targeting aldose reductase against diabetic complications: Bioactivity, cytotoxicity, and molecular modeling studies

Despite significant developments in therapeutic strategies, Diabetes Mellitus remains an increasing concern, leading to various complications, e.g., cataracts, neuropathy, retinopathy, nephropathy, and several cardiovascular diseases. The polyol pathway, which involves Aldose reductase (AR) as a critical enzyme, has been focused on by many researchers as a target for intervention. On the other hand, spiroindoline-based compounds possess remarkable biological properties. This guided us to synthesize novel spiroindoline oxadiazolyl-based acetate derivatives and investigate their biological activities. The synthesized molecules' structures were confirmed herein, using IR, NMR (1H and 13C), and Mass spectroscopy. All compounds were potent inhibitors with KI constants spanning from 0.186 ± 0.020 μM to 0.662 ± 0.042 μM versus AR and appeared as better inhibitors than the clinically used drug, Epalrestat (EPR, KI: 0.841 ± 0.051 μM). Besides its remarkable inhibitory profile compared to EPR, compound 6k (KI: 0.186 ± 0.020 μM) was also determined to have an unusual pharmacokinetic profile. The results showed that 6k had less cytotoxic effect on normal mouse fibroblast (L929) cells (IC50 of 569.58 ± 0.80 μM) and reduced the viability of human breast adenocarcinoma (MCF-7) cells (IC50 of 110.87 ± 0.42 μM) more than the reference drug Doxorubicin (IC50s of 98.26 ± 0.45 μM and 158.49 ± 2.73 μM, respectively), thus exhibiting more potent anticancer activity. Moreover, molecular dynamic simulations for 200 ns were conducted to predict the docked complex's stability and reveal significant amino acid residues that 6k interacts with throughout the simulation.

Sulfonyl thiourea derivatives from 2-aminodiarylpyrimidines: In vitro and in silico evaluation as potential carbonic anhydrase I, II, IX, and XII inhibitors

A series of synthesized sulfonyl thiourea derivatives (7a-o) of substituted 2-amino-4,6-diarylpyrimidines (4a-o) exhibited the remarkable inhibitory activity against some the human carbonic anhydrases (hCAs), including hCA I, II, IX, and XII isoforms. The inhibitory efficacy of synthesized sulfonyl thiourea derivatives were experimentally validated by in vitro enzymatic assays. 7a (KI  = 46.14 nM), 7j (KI  = 48.92 nM), and 7m (KI  = 62.59 nM) (for isoform hCA I); 7f (KI  = 42.72 nM), 7i (KI  = 40.98 nM), and 7j (KI  = 33.40 nM) (for isoform hCA II); 7j (KI  = 228.5 nM), 7m (KI  = 195.4 nM), and 7n (KI  = 210.1 nM) (for isoform hCA IX); 7l (KI  = 116.9 nM), 7m (KI  = 118.8 nM), and 7n (KI  = 147.2 nM) (for isoform hCA XII) in comparison with KI values of 452.1, 327.3, 437.2, and 338.9 nM, respectively, of the standard drug AAZ. These compounds also had significantly more potent inhibitory action against cytosolic isoform hCA I and tumor-associated isoforms hCA IX and hCA XII. Furthermore, the potential inhibitory compounds were subjected to in silico screening for molecular docking and molecular dynamics simulations. The results of in vitro and in silico studies revealed that compounds 7a, 7j, and 7m were the most promising derivatives in this series due to their significant effects on studied hCA I, II, IX, and XII isoforms, respectively. The results showed that the sulfonyl thiourea moiety was accommodated deeply in the active site and interacted with the zinc ion in the receptors.

An atomic surface site interaction point description of non-covalent interactions

Molecular electrostatic potential surfaces (MEPS) calculated using density functional theory have been used to develop a simplified description of the non-covalent interaction properties of organic molecules. The Atomic Interaction Point (AIP) model introduced here represents an evolution of the Surface Site Interaction Point (SSIP) model described previously, in which a molecule is represented by a discrete set of interaction points that define sites of interaction with other molecules. The interaction sites are described by interaction parameters that are equivalent to the experimentally determined H-bond donor and acceptor parameters α and β. By using high electron density MEPS that lie inside the van der Waals surface, it is possible to obtain accurate interaction parameters and locations for polar sites (s-holes, H-bond donors and acceptors), which are identified as local maxima and minima on the MEPS. For non-polar sites that represent π-systems and halogens, an approach based on molecular orbitals was used to assign the locations of the AIPs, and the interaction parameters were obtained using a lower electron density MEPS that lies close to the van der Waals surface. The AIP descriptions can be implemented directly in the Surface Site Interaction Point Model for Liquids at Equilibrium (SSIMPLE) to calculate solvation free energies, and the free energy of transfer of 1504 compounds from n-hexadecane to water was predicted with a root mean square error of 5 kJ mol-1. AIPs also provide a useful tool for mapping non-covalent interactions in intermolecular complexes, and examples are provided showing how X-ray crystal structures can be converted into AIP interaction maps that allow quantification of the free energy contributions of both polar and non-polar interactions to the stabilities of complexes in solution.

Synthesis, characterization and docking studies of benzenesulfonamide derivatives containing 1,2,3-triazole as potential ınhibitor of carbonic anhydrase I-II enzymes

Carbonic Anhydrases (CAs) are an important family of metalloenzymes that contain zinc (Zn2+) ions in their active site and catalyze the conversion of carbon dioxide to bicarbonate and proton and found in all living organisms. Sulfonamides are well-known inhibitors of CAs isoenzymes. In this study, a series of benzenesulfonamide derivatives (9a-h) containing 1,2,3-triazole-moiety were designed, synthesized and their structures were characterized by spectroscopic methods. In addition, molecular structures of compounds 5a, 5 b, 9e and 9f were elucidated by X-ray diffraction technique. To investigate drug similarity of 9a-h compounds, Lipinski's five rules (ADMET: absorption, distribution, metabolism, excretion and toxicity) were carried out by in silico studies. According to results, the compounds showed drug-like properties. Docking studies were applied to determine the scores, interactions and binding modes of compounds 9a-h against hCA I and hCA II enzymes. Compound 9c (-5.13 kcal/mol docking score) against hCA I enzyme and 9 h (-5.32 kcal/mol docking score) against hCA II enzyme showed potent inhibitory properties. The binding interactions of the compounds with the carbonic anhydrases were examined by docking studies.Communicated by Ramaswamy H. Sarma.

The Solvation Shell of Small Solutes in Aqueous-Organic Solvent Mixtures and Its Implications for Reversed-Phase Liquid Chromatography

Reversed-phase liquid chromatography (RPLC) operates with water-organic solvent (W-OS) mobile phases where preferential solvation (PS) of solutes is likely. To investigate the relevance of the solute solvation shell in the mobile phase for RPLC retention, we combine data from molecular dynamics simulations of small, neutral solutes (six analytes and two dead time markers) in W-methanol (MeOH) and W-acetonitrile (ACN) mixtures with corresponding retention data obtained on an RPLC column over a wide range of W/OS ratios. Data derived from Kirkwood-Buff integrals show PS by the OS for analytes vs low or negative PS for dead time markers. W-ACN mixtures generate a higher amount of PS than W-MeOH mixtures, which contributes to the higher eluent strength of ACN in RPLC. Difference spatial distribution functions reveal anisotropic solvation shells with OS excess at hydrocarbon elements and W excess at functional groups, predicting that retention by the hydrophobic stationary phase is favored by hydrocarbon elements and limited by functional groups. Analysis of solute-solvent hydrogen bonds pinpoints the hydrogen-bond requirements toward W as the retention-limiting factor. The relation between the solute solvation shell and retention confirms the importance of W-OS and solute-W hydrogen bonding for RPLC retention.

Solvation free energies of alcohols in water: temperature and pressure dependences

Solvation free energies μ* of amphiphilic species, methanol and 1,2-hexanediol, are obtained as a function of temperature or pressure based on molecular dynamics simulations combined with efficient free-energy calculation methods. In general, μ* of an amphiphile can be divided into and , the nonpolar and electrostatic contributions, and the former is further divided into and which are the work of cavity formation process and the free energy change due to weak, attractive interactions between the solute molecule and surrounding solvent molecules. We demonstrate that μ* of the two amphiphilic solutes can be obtained accurately using a perturbation combining method, which relies on the exact expressions for and and requires no simulations of intermediate systems between the solute with strong, repulsive interactions and the solute with the van der Waals and electrostatic interactions. The decomposition of μ* gives us several physical insights including that μ* is an increasing function of T due to , that the contributions of hydrophilic groups to the temperature dependence of μ* are additive, and that the contribution of the van der Waals attraction to the solvation volume is greater than that of the electrostatic interactions.

Synthesis, Theoretical, in Silico and in Vitro Biological Evaluation Studies of New Thiosemicarbazones as Enzyme Inhibitors

Eleven new thiosemicarbazone derivatives (1-11) were designed from nine different biologically and pharmacologically important isothiocyanate derivatives containing functional groups such as fluorine, chlorine, methoxy, methyl, and nitro at various positions of the phenyl ring, in addition to the benzyl unit in the molecular skeletal structure. First, their substituted-thiosemicarbazide derivatives were synthesized from the treatment of isothiocyanate with hydrazine to synthesize the designed compounds. Through a one-step easy synthesis and an eco-friendly process, the designed compounds were synthesized with yields of up to 95 % from the treatment of the thiosemicarbazides with aldehyde derivatives having methoxy and hydroxy groups. The structures of the synthesized molecules were elucidated with elemental analysis and FT-IR, 1 H-NMR, and 13 C-NMR spectroscopic methods. The electronic and spectroscopic properties of the compounds were determined by the DFT calculations performed at the B3LYP/6-311++G(2d,2p) level of theory, and the experimental findings were supported. The effects of some global reactivity parameters and nucleophilic-electrophilic attack abilities of the compounds on the enzyme inhibition properties were also investigated. They exhibited a highly potent inhibition effect on acetylcholinesterase (AChE) and carbonic anhydrases (hCAs) (KI values are in the range of 23.54±4.34 to 185.90±26.16 nM, 103.90±23.49 to 325.90±77.99 nM, and 86.15±18.58 to 287.70±43.09 nM for AChE, hCA I, and hCA II, respectively). Furthermore, molecular docking simulations were performed to explain each enzyme-ligand complex's interaction.

A least-squares-fitting procedure for an efficient preclinical ranking of passive transport across the blood-brain barrier endothelium

The treatment of various disorders of the central nervous system (CNS) is often impeded by the limited brain exposure of drugs, which is regulated by the human blood-brain barrier (BBB). The screening of lead compounds for CNS penetration is challenging due to the biochemical complexity of the BBB, while experimental determination of permeability is not feasible for all types of compounds. Here we present a novel method for rapid preclinical screening of libraries of compounds by utilizing advancements in computing hardware, with its foundation in transition-based counting of the flux. This method has been experimentally validated for in vitro permeabilities and provides atomic-level insights into transport mechanisms. Our approach only requires a single high-temperature simulation to rank a compound relative to a library, with a typical simulation time converging within 24 to 72 h. The method offers unbiased thermodynamic and kinetic information to interpret the passive transport of small-molecule drugs across the BBB.

Computational study on natural molecules targeting β-ketoacyl reductase domain of fatty acid synthase for the identification of selective inhibitors

Fatty acid synthase (FASN) enzyme is a lipid metabolism protein that provides the essential nutrients to cancer cells through de novo lipogenesis. Also, it plays a key role in other disease conditions, including obesity and inflammation. Hence, targeting the β-ketoacyl reductase (KR) domain of FASN protein, an in-silico study was performed on some selective bioactive natural molecules following a repurposing strategy to identify FASN inhibitors. A molecular docking study followed by Absorption, Distribution, Metabolism and Excretion (ADME) predictions, binding free energy calculations, and molecular dynamics (MD) simulations were performed against FASN protein (PDB ID:6NNA) using Schrodinger Drug Discovery Software. Compounds rutin, trans-chlorogenic acid, norbergenin, myricetin, quercetin, physalolactone, quercetin-3-O-galactoside, kaempferol, asperulosidic acid, luteolin, curcumin, 12-deoxywithastramonolide, pedunculoside, hernandifoline, and withafastuosin E were identified as hits, presenting better docking scores (-16.2, -14.1, -12.3, -12.1, -12.0, -11.3, -10.3, -9.8, -9.3, -9.2, -9.1, -8.5, -8.4, -8.3, -7.9, respectively) and hydrogen bond interactions with Ser 2021 and Tyr 2034 amino acids of the KR domain of FASN. The MD simulations study of top five hits in complex with protein 6NNA uncovered the significant interactions leading to the stabilization of ligand with Root Mean Square Deviation (RMSD) below 5.00 Å and the stability was further validated by evaluating the root mean square fluctuation, solvent accessible surface area, and radius of gyration graphs. Also, the FASN inhibition effect of top four hits (50 µM) was >50% when corroborated using High Performance Liquid Chromatography HPLC-based estimation of palmitic acid in MCF-7 cells. Thus rutin, trans-chlorogenic acid, norbergenin, and myricetin are proposed as prospective FASN inhibitory leads. Overall, the results provided useful modifications in pharmacophoric features that could improve the inhibitory effect.Communicated by Ramaswamy H. Sarma.

Energy-entropy multiscale cell correlation method to predict toluene-water log P in the SAMPL9 challenge

The energy-entropy multiscale cell correlation (EE-MCC) method is used to calculate toluene-water log P values of 16 drug molecules in the SAMPL9 physical properties challenge. EE-MCC calculates the free energy, energy and entropy from molecular dynamics (MD) simulations of the water and toluene solutions. Specifically, MCC evaluates entropy by partitioning the system into cells of correlated atoms at multiple length scales and further partitioning the local coordinates into energy wells, yielding vibrational and topographical terms from the energy-well sizes and probabilities. The log P values calculated by EE-MCC using three 200 ns MD simulations have a mean average error of 0.82 and standard error of the mean of 0.97 versus experiment, which is comparable with the best methods entered in SAMPL9. The main contribution to log P is from energy. Less polar drugs have more favourable energies of transfer. The entropy of transfer consists of increased solute vibrational and conformational terms in toluene due to weaker interactions, fewer solute positions in the larger-molecule solvent, reduced water vibrational entropy, negligible change in toluene vibrational entropy, and gains in solvent orientational entropy. The solvent entropy contributions here may be slightly underestimated because software limitations and statistical fluctuations meant that only the first shell could be included while averaged over the whole solution. Nonetheless, such issues will be addressed in future software to offer a general method to calculate entropy directly from MD simulation and to provide molecular understanding or guide system design.

Deciphering Molecular Aspects of Potential α-Glucosidase Inhibitors within Aspergillus terreus: A Computational Odyssey of Molecular Docking-Coupled Dynamics Simulations and Pharmacokinetic Profiling

Hyperglycemia, as a hallmark of the metabolic malady diabetes mellitus, has been an overwhelming healthcare burden owing to its high rates of comorbidity and mortality, as well as prospective complications affecting different body organs. Available therapeutic agents, with α-glucosidase inhibitors as one of their cornerstone arsenal, control stages of broad glycemia while showing definitive characteristics related to their low clinical efficiency and off-target complications. This has propelled the academia and industrial section into discovering novel and safer candidates. Herein, we provided a thorough computational exploration of identifying candidates from the marine-derived Aspergillus terreus isolates. Combined structural- and ligand-based approaches using a chemical library of 275 metabolites were adopted for pinpointing promising α-glucosidase inhibitors, as well as providing guiding insights for further lead optimization and development. Structure-based virtual screening through escalating precision molecular docking protocol at the α-glucosidase canonical pocket identified 11 promising top-docked hits, with several being superior to the market drug reference, acarbose. Comprehensive ligand-based investigations of these hits' pharmacokinetics ADME profiles, physiochemical characterizations, and obedience to the gold standard Lipinski's rule of five, as well as toxicity and mutagenicity profiling, proceeded. Under explicit conditions, a molecular dynamics simulation identified the top-stable metabolites: butyrolactone VI (SK-44), aspulvinone E (SK-55), butyrolactone I 4''''-sulfate (SK-72), and terrelumamide B (SK-173). They depicted the highest free binding energies and steadiest thermodynamic behavior. Moreover, great structural insights have been revealed, including the advent of an aromatic scaffold-based interaction for ligand-target complex stability. The significance of introducing balanced hydrophobic/polar moieties, like triazole and other bioisosteres of carboxylic acid, has been highlighted across docking, ADME/Tox profiling, and molecular dynamics studies for maximizing binding interactions while assuring safety and optimal pharmacokinetics for targeting the intestinal-localized α-glucosidase enzyme. Overall, this study provided valuable starting points for developing new α-glucosidase inhibitors based on nature-derived unique scaffolds, as well as guidance for prospective lead optimization and development within future pre-clinical and clinical investigations.

Synthesis and Characterization of Novel 1,3-Diaryltriazene-Substituted Sulfaguanidine Derivatives as Selective Carbonic Anhydrase Inhibitors: Biological Evaluation, in Silico ADME/T and Molecular Docking Study

Sulfonamide compounds known as human carbonic anhydrase (hCA) inhibitors are used in the treatment of many diseases such as epilepsy, antibacterial, glaucoma, various diseases. 1,3-diaryl-substituted triazenes and sulfaguanidine are used for therapeutic purposes in many drug structures. Based on these two groups, the synthesis of new compounds is important. In the present study, the novel 1,3-diaryltriazene-substituted sulfaguanidine derivatives (SG1-13) were synthesized and fully characterized by spectroscopic and analytic methods. Inhibitory effect of these compounds on the hCA I and hCA II was screened as in vitro. All the series of synthesized compounds have been identified as potential hCA isoenzymes inhibitory with KI values in the range of 6.44±0.74-86.85±7.01 nM for hCA I and with KI values in the range of 8.16±0.40-77.29±9.56 nM for hCA II. Moreover, the new series of compounds showed a more effective inhibition effect than the acetazolamide used as a reference. The possible binding positions of the compounds with a binding affinity to the hCA I and hCA II was demonstrated by in silico studies. In conclusion, compounds with varying degrees of affinity for hCA isoenzymes have been designed and as selective hCA inhibitors. These compounds may be potential alternative agents that can be used to treat or prevent diseases associated with glaucoma and hCA inhibition.

Marine drugs as putative inhibitors against non-structural proteins of SARS-CoV-2: an in silico study

INTRODUCTION

Coronavirus disease 2019 (COVID-19) is an unprecedented pandemic, threatening human health worldwide. The need to produce novel small-molecule inhibitors against the ongoing pandemic has resulted in the use of drugs such as chloroquine, azithromycin, dexamethasone, favipiravir, ribavirin, remdesivir and azithromycin. Moreover, the reports of the clinical trials of these drugs proved to produce detrimental effects on patients with side effects like nephrotoxicity, retinopathy, cardiotoxicity and cardiomyopathy. Recognizing the need for effective and non-harmful therapeutic candidates to combat COVID-19, we aimed to develop promising drugs against SARS-COV-2.

DISCUSSION

In the current investigation, high-throughput virtual screening was performed using the Comprehensive Marine Natural Products Database against five non-structural proteins: Nsp3, Nsp5, Nsp12, Nsp13 and Nsp15. Furthermore, standard precision (SP) docking, extra precision (XP) docking, binding free energy calculation and absorption, distribution, metabolism, excretion and toxicity studies were performed using the Schrӧdinger suite. The top-ranked 5 hits obtained by computational studies exhibited to possess a greater binding affinity with the selected non-structural proteins. Amongst the five hits, CMNPD5804, CMNPD20924 and CMNPD1598 hits were utilized to design a novel molecule (D) that has the capability of interacting with all the key residues in the pocket of the selected non-structural proteins. Furthermore, 200 ns of molecular dynamics simulation studies provided insight into the binding modes of D within the catalytic pocket of selected proteins.

CONCLUSION

Hence, it is concluded that compound D could be a promising inhibitor against these non-structural proteins. Nevertheless, there is still a need to conduct in vitro and in vivo studies to support our findings.

Binding Analysis and Structure-Based Design of Tricyclic Coumarin-Derived MTHFD2 Inhibitors as Anticancer Agents: Insights from Computational Modeling

Unfolded protein response (UPR)-dependent metabolic reprogramming diverts metabolites from glycolysis to mitochondrial 1C metabolism, highlighting pharmacological resistance to folate drugs and overexpression of certain enzymes. Methylenetetrahydrofolate dehydrogenase (MTHFD2) is a mitochondrial enzyme that plays a key role in 1C metabolism in purine and thymidine synthesis and is exclusively overexpressed in cancer cells but absent in most healthy adult human tissues. To the best of our knowledge, tricyclic coumarin-based compounds (substrate site binders) and xanthine derivatives (allosteric site binders) are the only selective inhibitors of MTHFD2 reported until the present date. The current study aims at the investigation of the available structural data of MTHFD2 in complex with potent and selective inhibitors that occupy the substrate binding site, further providing insights into binding mode, key protein-ligand interactions, and conformational dynamics, that correspond to the experimental binding affinities and biological activities. In addition, we carried out structure-based drug design on the substrate binding site of MTHFD2, by exploiting the cocrystal structure of MTHFD2 with the tricyclic coumarin-based inhibitor. The structure-based drug design campaign involves R-group enumeration, bioisostere replacement, molecular docking, ADME prediction, MM-GBSA binding free energy calculations, and molecular dynamics simulations, that led to a small library of new and potential compounds, capable of selectively inhibiting MTHFD2. The results reported herein are expected to benefit medicinal chemists working on the development of selective MTHFD2 inhibitors for cancer treatment, although experimental validation by biochemical and/or pharmacokinetic assays is required to substantiate the outcomes of the study.

Novel acetic acid derivatives containing quinazolin-4(3H)-one ring: Synthesis, in vitro, and in silico evaluation of potent aldose reductase inhibitors

Aldose reductase (AR) is a crucial enzyme of the polyol pathway through which glucose is metabolized under conditions of hyperglycemia related to diabetes. A series of novel acetic acid derivatives containing quinazolin-4(3H)-one ring (1-22) was synthesized and tested for in vitro AR inhibitory effect. All the target compounds exhibited nanomolar activity against the target enzyme, and all compounds displayed higher activity as compared to the reference drug epalrestat. Among them, Compound 19, named 2-(4-[(2-[(4-methylpiperazin-1-yl)methyl]-4-oxoquinazolin-3(4H)-ylimino)methyl]phenoxy)acetic acid, displayed the strongest inhibitory effect with a KI value of 61.20 ± 10.18 nM. Additionally, these compounds were investigated for activity against L929, nontumoral fibroblast cells, and MCF-7, breast cancer cells using the MTT assay. Compounds 16 and 19 showed lower toxicity against the normal L929 cells. The synthesized compounds' (1-22) absorption, distribution, metabolism, and excretion properties were also evaluated. Molecular docking simulations were used to look into the possible binding mechanisms of these inhibitors against AR.

Design, synthesis and evaluation of 5-chloro-6-methylaurone derivatives as potential anti-cancer agents

A series of novel 5-chloro-6-methylaurone derivatives (6a-p) were synthesized and characterized by various spectroscopic techniques. The synthesized compounds were tested for anticancer activity against 60-human cancer cell line panel derived from nine cancer types at NCI, Bethesda, USA. Among the synthesized compounds, six compounds (6e, 6f, 6h, 6i, 6k and 6 m) exhibited growth inhibition and cytotoxic activity against various human cancer cell lines in one-dose data. The most potent compound among the series, 6i was active against 55 out of 60 human cancer cell lines. Compound 6i showed remarkable % growth inhibition and cytotoxicity against various cancer cell lines exhibiting % GI in the range 36.05-199.03. The compound 6i was further evaluated for five dose assay and exhibited GI50 1.90 µM and 2.70 µM against melanoma and breast cancer cell lines respectively. Further evaluation of 6i for five-dose assay exhibited a diverse spectrum of anti-cancer activity towards all the 60 human cancer cell line panel with the selectivity index ratio ranging 0.854-1.42  and 0.66-1.35  for GI50 and TGI respectively. Based on one-dose and five-dose data compound 6i was further evaluated for cell apoptosis against MDA-MB-468 breast cancer cell line and was found to induce early apoptosis in cells explaining its mode of action. The in-silico studies for the synthesized compounds as LSD1 inhibitors (2H94) have shown better docking score and binding energy comparable to vafidemstat. All the compounds followed Lipinski rule of five. These findings concluded that the compound 6i could lead to the development of a promising therapeutic anticancer agent.

Discovery of novel benzenesulfonamides incorporating 1,2,3-triazole scaffold as carbonic anhydrase I, II, IX, and XII inhibitors

Sulfonamides are among the most promising potential inhibitors for carbonic anhydrases (CAs), which are pharmaceutically relevant targets for treating several disease conditions. Herein, a series of benzenesulfonamides bearing 1,2,3-triazole moiety as inhibitors of human (h) α-CAs (hCAs) were designed using the tail approach. The design method combines a benzenesulfonamide moiety with a tail of oxime and a zinc-binding group on a 1,2,3-triazole scaffold. Among the synthesized derivatives, the naphthyl (6m, K_I of 68.6 nM, S_I of 10.3), and methyl (6a, K_I of 56.3 nM, S_I of 11.7) derivatives (over hCA IX) and propyl (6c, K_I of 95.6 nM, S_I of 2.7), and pentyl (6d, K_I of 51.1 nM, S_I of 6.6) derivatives (over hCA XII) displayed a noticeable selectivity for isoforms hCA I and II, respectively. Meanwhile, derivative 6e displayed a potent inhibitory effect versus the cytosolic isoform hCA I (K_I of 47.8 nM) and tumor-associated isoforms hCA IX and XII (K_Is of 195.9 and 116.9 nM, respectively) compared with the reference drug acetazolamide (AAZ, K_Is of 451.8, 437.2, and 338.9 nM, respectively). Derivative 6b showed higher potency (K_I of 33.2 nM) than AAZ (K_I of 327.3 nM) towards another cytosolic isoform hCA II. Nevertheless, substituting the lipophilic large naphthyl tail to the 1,2,3-triazole linked benzenesulfonamides (6a-n) raised inhibitory effect versus hCA I and XII and selectivity towards hCA I and II isoforms over hCA IX. Evaluation of the cytotoxic potential of the synthesized derivatives was conducted in L929, MCF-7, and Hep-3B cell lines. Several compounds in the series demonstrated significant antiproliferative activity and minimal cytotoxicity. In the molecular docking study, the sulfonamide moiety interacted with the zinc-ion and neatly fit into the hCAs active sites. The extension of the tail was found to participate in diverse hydrophilic and hydrophobic interactions with adjacent amino acids, ultimately influencing the effectiveness and specificity of the derivatives.

Quantum-Mechanical Approach to Predicting the Carcinogenic Potency of N-Nitroso Impurities in Pharmaceuticals

N-Nitroso contaminants in medicinal products are of concern due to their high carcinogenic potency; however, not all these compounds are created equal, and some are relatively benign chemicals. Understanding the structure-activity relationships (SARs) that drive hazards in one molecule versus another is key to both protecting human health and alleviating costly and sometimes inaccurate animal testing. Here, we report on an extension of the CADRE (computer-aided discovery and REdesign) platform, which is used broadly by the pharmaceutical and personal care industries to assess environmental and human health endpoints, to predict the carcinogenic potency of N-nitroso compounds. The model distinguishes compounds in three potency categories with 77% accuracy in external testing, which surpasses the reproducibility of rodent cancer bioassays and constraints imposed by limited (high-quality) data. The robustness of predictions for more complex pharmaceuticals is maximized by capturing key SARs using quantum mechanics, that is, by hinging the model on the underlying chemistry versus chemicals in the training set. To this end, the present approach can be leveraged in a quantitative hazard assessment and to offer qualitative guidance using electronic structure comparisons between well-studied analogues and unknown contaminants.

Pyrimidines: Molecular docking and inhibition studies on carbonic anhydrase and cholinesterases

Alzheimer's disease (AD) is a neurodegenerative disorder. The disease is characterized by dementia, memory impairment, cognitive impairment, and speech impairment. Cholinesterases (ChEs; AChE, acetylcholinesterase and BChE, butyrylcholinesterase) inhibitors and their benefits of cholinergic replacement in the treatment of AD have been researched and documented by scientists in various ways to date. Recent studies prove that human carbonic anhydrases (hCAs) are also one of the important targets in the treatment of AD. Therefore, the development of new agents that can simultaneously modulate the various mechanisms or targets involved in the AD pathway may be a powerful strategy to treat AD, the current disease. Considering these data, the effects of the pyrimidines (1-7) were investigated in this study for the discovery and development of multitargeted ChEs and hCAs inhibitors associated with AD. In addition, the molecular docking analysis of the 4-amino-2-choloropyrimidine (2) was performed to understand the binding interactions on the active site of the enzyme. All compounds (1-7) showed satisfactory enzyme inhibitory potency in micromolar concentrations against AChE, BChE, hCAI, and hCAII with K_I values ranging from 0.099 to 0.241 μM, from 1.324 to 3.418 μM, from 0.201 to 0.884 μM, from 1.867 to 3.913 μM, respectively. Due to their ChEs and hCAs inhibition, these compounds (1-7) may be considered as leads for investigations in neurodegenerative diseases. All these results revealed that the 4-amino-5,6-dichloropyrimidine (7) (K_I value of 0.201 ± 0.041 μM for hCA I), the 4-amino-6-hydroxypyrimidine (4) (K_I value of 1.867 ± 0.296 μM for hCA II), the 4-amino-5,6-dichloropyrimidine (7) (K_I value of 0.099 ± 0.008 μM for AChE), and the 4-amino-2-chloropyrimidine (2) (K_I value of 1.324 ± 0.273 μM for BChE) from the pyrimidines in this series were the most promising derivatives, as they exhibited a good multifunctional inhibition at all experimental levels and in the in silico validation against these enzymes, for the treatment of AD.

Molecular and Biological Investigation of Isolated Marine Fungal Metabolites as Anticancer Agents: A Multi-Target Approach

Cancer is the leading cause of death globally, with an increasing number of cases being annually reported. Nature-derived metabolites have been widely studied for their potential programmed necrosis, cytotoxicity, and anti-proliferation leading to enrichment for the modern medicine, particularly within the last couple of decades. At a more rapid pace, the concept of multi-target agents has evolved from being an innovative approach into a regular drug development procedure for hampering the multi-fashioned pathophysiology and high-resistance nature of cancer cells. With the advent of the Red Sea Penicillium chrysogenum strain S003-isolated indole-based alkaloids, we thoroughly investigated the molecular aspects for three major metabolites: meleagrin (MEL), roquefortine C (ROC), and isoroquefortine C (ISO) against three cancer-associated biological targets Cdc-25A, PTP-1B, and c-Met kinase. The study presented, for the first time, the detailed molecular insights and near-physiological affinity for these marine indole alkaloids against the assign targets through molecular docking-coupled all-atom dynamic simulation analysis. Findings highlighted the superiority of MEL's binding affinity/stability being quite in concordance with the in vitro anticancer activity profile conducted via sulforhodamine B bioassay on different cancerous cell lines reaching down to low micromolar or even nanomolar potencies. The advent of lengthy structural topologies via the metabolites' extended tetracyclic cores and aromatic imidazole arm permitted multi-pocket accommodation addressing the selectivity concerns. Additionally, the presence decorating polar functionalities on the core hydrophobic tetracyclic ring contributed compound's pharmacodynamic preferentiality. Introducing ionizable functionality with more lipophilic characters was highlighted to improve binding affinities which was also in concordance with the conducted drug-likeness/pharmacokinetic profiling for obtaining a balanced pharmacokinetic/dynamic profile. Our study adds to the knowledge regarding drug development and optimization of marine-isolated indole-based alkaloids for future iterative synthesis and pre-clinical investigations as multi-target anticancer agents.

Exploration of 1,2,3-triazole linked benzenesulfonamide derivatives as isoform selective inhibitors of human carbonic anhydrase

A novel series of 1,2,3-triazole benzenesulfonamide substituted 1,3-dioxoisoindolin-5-carboxylate (7a-l) inhibitors of human α-carbonic anhydrase (hCA) was designed using a tail approach. The design method relies on the hybridization of a benzenesulfonamide moiety with a tail of 1,3-dioxoisoindoline-5-carboxylate and a zinc-binding group on a 1,2,3-triazole scaffold. Among the synthesized analogues, 2‑iodophenyl (7f, K_I of 105.00 nM and S_I of 2.98) and 2‑naphthyl (7h, K_I of 32.11 nM and S_I of 3.48) analogues (over off-target hCA I) and phenyl (7a, K_I of 50.13 nM and S_I of 2.74) and 2,6‑dimethylphenyl (7d, K_I of 50.60 nM and S_I of 3.35) analogues (over off-target hCA II) exhibited a remarkable selectivity for tumor isoforms hCA IX and XII, respectively. Meanwhile, analogue 7a displayed a potent inhibitory effect against the tumor-associated isoform hCA IX (K_I of 18.29 nM) compared with the reference drug acetazolamide (AAZ, K_I of 437.20 nM), and analogue 7h showed higher potency (K_I of 9.22 nM) than AAZ (K_I of 338.90 nM) against another tumor-associated isoform hCA XII. However, adding the lipophilic large naphthyl tail to the 1,3-dioxoisoindolin-5-carboxylate analogues increased both the hCA inhibitory and selective activities against the target isoform, hCA XII. Additionally, these analogues (7a-l) showed IC₅₀ values against the human lung (A549) adenocarcinoma cancer cell line ranging from 129.71 to 352.26 μM. The results of the molecular docking study suggested that the sulfonamide moiety fits snugly into the hCAs active sites and interacts with the Zn²⁺ ion. At the same time, the tail extension engages in various hydrophilic and hydrophobic interactions with the nearby amino acids, which affects the potency and selectivity of the hybrids.

Molecular Docking Studies and the Effect of Fluorophenylthiourea Derivatives on Glutathione-Dependent Enzymes

Cancer is a serious problem affecting the health of all human societies. Chemotherapy refers to the use of drugs to kill cancer or the origin of cancer. In the past three decades, researchers have studied about proteins and their roles in the production of cancer cells. Glutathione S-transferases (GSTs) are a superfamily of enzymes that play a key role in cellular detoxification, protecting against reactive electrophiles attacks, including chemotherapeutic agents. Glutathione reductase (GR) is an important antioxidant enzyme involved in protecting the cell against oxidative stress. In this current study, GST and GR enzymes were purified from human erythrocytes using affinity chromatography. GR was obtained with a specific activity of 5.95 EU/mg protein and a 52.38 % yield. GST was obtained with a specific activity of 4.88 EU/mg protein and a 74.88 % yield. The effect of fluorophenylthiourea derivatives on the purified enzymes was investigated. Afterward, K_I values were found to range from 23.04±4.37 μM-59.97±13.45 μM for GR and 7.22±1.64 μM-41.24±2.55 μM for GST. 1-(2,6-difluorophenyl)thiourea was showed the best inhibition effect for both GST and GR enzymes. The relationships of inhibitors with 3D structures of GST and GR were explained by molecular docking studies.

Enzyme inhibition, molecular docking, and density functional theory studies of new thiosemicarbazones incorporating the 4-hydroxy-3,5-dimethoxy benzaldehyde motif

New Schiff base-bearing thiosemicarbazones (1-13) were obtained from 4-hydroxy-3,5-dimethoxy benzaldehyde and various isocyanates. The structures of the synthesized molecules were elucidated in detail. Density functional theory calculations were also performed to determine the spectroscopic properties of the compounds. Moreover, the enzyme inhibition activities of these compounds were investigated. They showed highly potent inhibition effects on acetylcholinesterase (AChE) and human carbonic anhydrases (hCAs) (K_I values are in the range of 51.11 ± 6.01 to 278.10 ± 40.55 nM, 60.32 ± 9.78 to 300.00 ± 77.41 nM, and 64.21 ± 9.99 to 307.70 ± 61.35 nM for AChE, hCA I, and hCA II, respectively). In addition, molecular docking studies were performed, confirmed by binding affinities studies of the most potent derivatives.

Molecular docking and inhibition studies of vulpinic, carnosic and usnic acids on polyol pathway enzymes

Aldose reductase (AR) and sorbitol dehydrogenase (SDH) are important enzymes of the polyol pathway. In the current study, inhibitory effects of vulpinic acid (VA) carnosic acid (CA) and usnic acid (UA) on purified AR and SDH enzymes were determined. These enzymes inhibition could be essential to prevent diabetic complications. AR and SDH enzymes were purified from sheep kidney. Then, VA, CA and UA were tested in various concentrations against these enzymes activity in vitro. K_I values were found to be as 1.46 ± 0.04, 5.13 ± 0.25 and 11.71 ± 0.27 μΜ for VA, CA and UA, respectively, for AR. K_I constants were found to be as 15.32 ± 0.34, 145.60 ± 2.17 and 213.40 ± 2.64 μΜ VA, CA and UA, respectively, for SDH. These findings indicate that VA, CA and UA could be useful in the treatment of diabetic complications.Communicated by Ramaswamy H. Sarma.

Finding potential inhibitors against RNA-dependent RNA polymerase (RdRp) of bovine ephemeral fever virus (BEFV): an in-silico study

The bovine ephemeral fever virus (BEFV) is an enzootic agent that affects millions of bovines and causes major economic losses. Though the virus is seasonally reported with a very high morbidity rate (80-100%) from African, Australian, and Asiatic continents, it remains a neglected pathogen in many of its endemic areas, with no proper therapeutic drugs or vaccines presently available for treatment. The RNA-dependent RNA polymerase (RdRp) catalyzes the viral RNA synthesis and is an appropriate candidate for antiviral drug developments. We utilized integrated computational tools to build the 3D model of BEFV-RdRp and then predicted its probable active binding sites. The virtual screening and optimization against these active sites, using several small-molecule inhibitors from a different category of Life Chemical database and FDA-approved drugs from the ZINC database, was performed. We found nine molecules that have docking scores varying between -6.84 to -10.43 kcal/mol. Furthermore, these complexes were analyzed for their conformational dynamics and thermodynamic stability using molecular dynamics simulations in conjunction with the molecular mechanics generalized Born surface area (MM-GBSA) scheme. The binding free energy calculations depict that the electrostatic interactions play a dominant role in the RdRp-inhibitor binding. The hot spot residues, such as Arg565, Asp631, Glu633, Asp740, and Glu707, were found to control the RdRp-inhibitor interaction. The ADMET analysis strongly suggests favorable pharmacokinetics of these compounds that may prove useful for treating the BEFV ailment. Overall, we anticipate that these findings would help explore and develop a wide range of anti-BEFV therapy.Communicated by Ramaswamy H. Sarma.

The surface site interaction point approach to non-covalent interactions

The functional properties of molecular systems are generally determined by the sum of many weak non-covalent interactions, and therefore methods for predicting the relative magnitudes of these interactions is fundamental to understanding the relationship between function and structure in chemistry, biology and materials science. This review focuses on the Surface Site Interaction Point (SSIP) approach which describes molecules as a set of points that capture the properties of all possible non-covalent interactions that the molecule might make with another molecule. The first half of the review focuses on the empirical non-covalent interaction parameters, α and β, and provides simple rules of thumb to estimate free energy changes for interactions between different types of functional group. These parameters have been used to have been used to establish a quantitative understanding of the role of solvent in solution phase equilibria, and to describe non-covalent interactions at the interface between macroscopic surfaces as well as in the solid state. The second half of the review focuses on a computational approach for obtaining SSIPs and applications in multi-component systems where many different interactions compete. Ab initio calculation of the Molecular Electrostatic Potential (MEP) surface is used to derive an SSIP description of a molecule, where each SSIP is assigned a value equivalent to the corresponding empirical parameter, α or β. By considering the free energies of all possible pairing interactions between all SSIPs in a molecular ensemble, it is possible to calculate the speciation of all intermolecular interactions and hence predict thermodynamic properties using the SSIMPLE algorithm. SSIPs have been used to describe both the solution phase and the solid state and provide accurate predictions of partition coefficients, solvent effects on association constants for formation of intermolecular complexes, and the probability of cocrystal formation. SSIPs represent a simple and intuitive tool for describing the relationship between chemical structure and non-covalent interactions with sufficient accuracy to understand and predict the properties of complex molecular ensembles without the need for computationally expensive simulations.

N-substituted phthalazine sulfonamide derivatives as non-classical aldose reductase inhibitors

Aldose reductase (AR, AKR1B1; EC 1.1.1.21) is an aldo-keto reductase that has been widely investigated as an enzyme crucially involved in the pathogenesis of several chronic complications, including nephropathy, neuropathy, retinopathy, and cataracts associated with diabetes mellitus. Although sulfonamides have been reported to possess many other biological activities, in continuation of our interest in designing and discovering potent inhibitors of AR, herein, we have evaluated the AR inhibitory potential of N-substituted phthalazine sulfonamide derivatives 5a-l. The biological studies revealed that all the derivatives show excellent activity against AR, with K_I constants ranging from 67.73 to 495.20 nM. Among these agents, 4-(6-nitro-1,4-dioxo-1,2,3,4-tetrahydrophthalazine-2-carbonyl)benzenesulfonamide (5e) and 1,4-dioxo-3-(4-sulfamoylbenzoyl)-1,2,3,4-tetrahydrophthalazine-6-carboxylic acid (5f) showed prominent inhibitory activity with K_I values of 67.73 and 148.20 nM, respectively, vs AR and were found to be more potent than epalrestat (K_I  = 852.50 nM), the only AR inhibitor currently used in the therapy. Moreover, molecular docking studies were also performed to rationalize binding site interactions of these sulfonamides (5a-l) with the target enzyme AR. According to ADME-Tox, predicts were also determined that these derivatives be ARIs displaying suitable drug-like properties. The sulfonamides identified in this study may be used to develop lead therapeutic agents inhibiting diabetic complications.

Biogenic synthesis of ZnO nanoparticles mediated from Borassus flabellifer (Linn): antioxidant, antimicrobial activity against clinical pathogens, and photocatalytic degradation activity with molecular modeling

Borassus flabellifer leaf extract has been used for rapid biogenic synthesis of zinc oxide nanoparticles (ZnO-NPs) due to rich source of bioactive compounds. The synthesized ZnO-NPs were preliminarily confirmed by UV-visible spectroscopy adsorption peak range at 365 nm. The XRD (X-ray diffraction) confirms purity of ZnO-NPs that were crystalline in nature. The analysis of FT-IR (Fourier-transform infrared spectroscopy) confirms the presence of the following functional group such as alcohol, phenols, carboxylic acids, primary amides, secondary amides, and alkyl halide. The Field Emission Scanning Electron Microscope (FE-SEM) analysis indicated that ZnO-NPs were in spherical shape, followed by EDX analysis which confirmed the presence of Zn-element. Antimicrobial effect of ZnO-NPs was investigated using different clinical pathogens like bacteria Staphylococcus aureus, Bacillus subtilis, Escherichia coli, Klebsiella Pneumonia, and Pseudomonas aeruginosa and fungi Aspergillus flavus, Candida albicans, and Penicillium expansum which confirmed ZnO-NPs efficiency as an antimicrobial agent. ZnO-NP antimicrobial efficiency was observed in higher zone of inhibition at 50 μg/mL concentrations. Antioxidant activity was ascertained to be used for several biomedical applications. The ZnO-NPs efficiently degraded the environmental toxic dyes (methylene blue and crystal violet) under sunlight, and up to 95% higher degradation was achieved in both dyes. In support of photo light degradation, the study was progressed to understand the ZnO-dye interaction stability using molecular mechanism, and it shows efficient bonding features in the NPs environment. Overall, this investigation has great potential for being an effective and eco-friendly material used in environmental applications.

Polyfunctionalized α-Phenyl-tert-butyl(benzyl)nitrones: Multifunctional Antioxidants for Stroke Treatment

Nowadays, most stroke patients are treated exclusively with recombinant tissue plasminogen activator, a drug with serious side effects and limited therapeutic window. For this reason, and because of the known effects of oxidative stress on stroke, a more tolerable and efficient therapy for stroke is being sought that focuses on the control and scavenging of highly toxic reactive oxygen species by appropriate small molecules, such as nitrones with antioxidant properties. In this context, herein we report here the synthesis, antioxidant, and neuroprotective properties of twelve novel polyfunctionalized α-phenyl-tert-butyl(benzyl)nitrones. The antioxidant capacity of these nitrones was investigated by various assays, including the inhibition of lipid peroxidation induced by AAPH, hydroxyl radical scavenging assay, ABTS+-decoloration assay, DPPH scavenging assay, and inhibition of soybean lipoxygenase. The inhibitory effect on monoamine oxidases and cholinesterases and inhibition of β-amyloid aggregation were also investigated. As a result, (Z)-N-benzyl-1-(2-(3-(piperidin-1-yl)propoxy)phenyl)methanimine oxide (5) was found to be one of the most potent antioxidants, with high ABTS+ scavenging activity (19%), and potent lipoxygenase inhibitory capacity (IC50 = 10 µM), selectively inhibiting butyrylcholinesterase (IC50 = 3.46 ± 0.27 µM), and exhibited neuroprotective profile against the neurotoxicant okadaic acid in a neuronal damage model. Overall, these results pave the way for the further in-depth analysis of the neuroprotection of nitrone 5 in in vitro and in vivo models of stroke and possibly other neurodegenerative diseases in which oxidative stress is identified as a critical player.

Human Apparent Volume of Distribution Predicts Bioaccumulation of Ionizable Organic Chemicals in Zebrafish Embryos

Chemicals with elevated bioaccumulation profiles present potential hazards to public health and the environment. Ionizable organic compounds (IOCs) increasingly represent a large proportion of commercial chemicals; however, historical approaches for bioaccumulation determinations are mainly developed for neutral chemicals, which were not appropriate for IOCs. Herein, we employed the zebrafish embryo, a common vertebrate model in environmental and biomedical studies, to elucidate toxicokinetics and bioconcentration of eight IOCs with diverse physicochemical properties and pharmacokinetic parameters. At an environmentally relevant pH (7.5), most IOCs exhibited rapid uptake and depuration in zebrafish, suggesting the ionized forms of IOCs are readily bioavailable. Bioconcentration factors (BCF) of these IOCs ranged from 0.0530 to 250 L·kg^-1 wet weight. The human pharmacokinetic proportionality factor, apparent volume of distribution (V_D), better predicted the BCF of selected IOCs than more commonly used hydrophobicity-based parameters (e.g., pH-dependent octanol-water distribution ratio, D_ow). Predictive bioaccumulation models for IOCs were constructed and validated using V_D alone or with D_ow. Significant relationships between fish BCF and human V_D, which is readily available for pharmaceuticals, highlighted the utility of biologically based "read-across" approaches for predicting bioaccumulative potential of IOCs. Our novel findings thus provided an understanding of the partitioning behavior and improved predictive bioconcentration modeling for IOCs.

Biological evaluation and in silico study of benzohydrazide derivatives as paraoxonase 1 inhibitors

Serum paraoxonase 1 (PON1) is found in all mammalian species and is a calcium-dependent hydrolytic enzyme. PON1 hydrolyze several substrates, including carbonates, esters, and organophosphates. In the current study, we aimed to investigate the effect of the presynthesized benzohydrazide derivatives (1-9) on PON1 activity. Benzohydrazide compounds moderate inhibited PON1 with the half-maximal inhibitory concentration values ranging from 76.04 ± 13.51 to 221.70 ± 13.59 μM and K_I values ranging from 38.75 ± 12.21 to 543.50 ± 69.76 μM. Compound 4 (2-amino-4-chlorobenzohydrazide) showed the best inhibition (K_I  = 38.75 ± 12.21 μM). Molecular docking and ADME-Tox studies of benzohydrazide derivatives were also carried out. In this context, we hope that the results obtained in this study contribute to the determination of the side effects of current and new benzohydrazide-based pharmacological compounds to be developed.

Identification of potential inhibitors, conformational dynamics, and mechanistic insights into mutant Kirsten rat sarcoma virus (G13D) driven cancers

The mutations at the hotspot region of K-Ras result in the progression of cancer types. Our study aimed to explore the small molecule inhibitors against the G13D mutant K-Ras model with anti-cancerous activity from food and drug administration (FDA)-approved drug compounds. We implemented several computational strategies such as pharmacophore-based virtual screening, molecular docking, absorption, distribution, metabolism and excretion features, and molecular simulation to ensure the identified hit compounds have potential efficacy against G13D K-Ras. We found that the FDA-approved compounds, namely, azelastine, dihydrocodeine, paroxetine, and tramadol, are potential candidates to inhibit the action of G13D mutant K-Ras. All four compounds exhibited similar binding patterns of sotorasib, and a structural binding mechanism with significant hydrophobic contacts. The descriptor features from the QikProp of all four compounds are within allowable limits compared to sotorasib drug. Consequently, a molecular simulation result emphasized that the dihydrocodeine and tramadol exhibited less fluctuation, minimal basin, significant h-bonds, and potent inhibition against G13D K-Ras. As a result, the current research identifies prospective K-Ras inhibitors that could be further improved with biochemical analysis for precision medicine against K-Ras-driven cancers.

Methyl benzoate derivatives: in vitro Paraoxonase 1 inhibition and in silico studies

Paraoxonase 1 (PON1) can metabolize some compounds such as aromatic carboxylic acid and unsaturated aliphatic esters, arylesters, cyclic carbonate, plucuronide drugs, some carbamate insecticide classes, nerve gases, and lactone compounds. Methyl benzoate has recently been shown to display potent toxicity against several insect species. In the current study, we aimed to investigate the effect of the methyl benzoate compounds (1-17) on PON1 activity. Methyl benzoate compounds inhibited PON1 with K_I values ranging from 25.10 ± 4.73 to 502.10 ± 64.72 μM. Compound 10 (methyl 4-amino-2-bromo benzoate) showed the best inhibition (K_I  = 25.10 ± 4.73 μM). Furthermore, using the ADME-Tox, Glide XP, and MM-GBSA tools of the Schrödinger Suite 2021-4, a complete ligand-receptor interaction prediction was performed to characterize the methyl benzoates (1-17), probable binding modalities versus the PON1.

Prediction of binding affinity of 1,2-diphenyline ketone analogues at adenosine triphosphate binding site of glycogen synthase kinase-3β: a molecular docking and dynamic simulation study

Glycogen synthase kinase (GSK)-3β is one of the downstream signalling molecules involved in phosphorylation of glycogen synthase, a key enzyme involved in the synthesis of glycogen from glucose. GSK-3β regulate some of the critical processes underlying structural and functional synaptic plasticity of neurons. Down regulation or inhibition of GSK-3β enhances long-term potentiation and cognitive functions in animal models of Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. A number of compounds are available to inhibit GSK-3β, however none of them are in clinical practice to treat neurodegenerative diseases. The aim of our study was to predict the molecular interaction and dynamic behaviour of naturally occurring 1,2-diphenyline ketone analogues at the adenosine triphosphate binding site of glycogen synthase kinase (GSK)-3β through simulation studies. Out of all 1,2-diphenyline ketone analogues,1, 3, 5, 6-Tetrahydroxyxanthone (Rank = 1), Secalonic acid F (Rank = 2), and Trihydroxy-2-(2,3-dihydroxy-3-methylbutyl)-7-methoxy-8-(3-methyl-2-butenyl) xanthone (Rank = 3) were found to exhibit lowest docking score of -12.07, -11.49, and -11.24 kcal/mol with dissociation constant of 1.37, 3.84, and 5.99 nM, respectively. The molecular dynamic simulation of rank 1 and rank 3 ligands indicated stable interaction throughout the simulation and interaction analyses has shown that the presence of hydroxyl groups at C1, C3, C5, and C6 around 1,2 diphenyline ketone nucleus to influence their binding affinity at the ATP-binding site of GSK-3β. We predicted that 1,3,5,6-Tetrahydroxyxanthone and 1, 3, 6-Trihydroxy-2-(2,3-dihydroxy-3-methylbutyl)-7-methoxy-8-(3-methyl-2-butenyl) xanthone may act as a potential ligand or lead compound to inhibit GSK-3β and also may play an important role in alleviating neurodegenerative diseases.Communicated by Ramaswamy H. Sarma.

Design, Semisynthesis, and Estrogenic Activity of Lignan Derivatives from Natural Dibenzylbutyrolactones

Based on molecular docking studies on the ERα, a series of lignan derivatives (3–16) were designed and semisynthesized from the natural dibenzylbutyrolactones bursehernin (1) and matairesinol dimethyl ether (2). To examine their estrogenic and antiestrogenic potencies, the effects of these compounds on estrogen receptor element (ERE)-driven reporter gene expression and viability in human ER+ breast cancer cells were evaluated. Lignan compounds induced ERE-driven reporter gene expression with very low potency as compared with the pure agonist E2. However, coincubation of 5 μM of lignan derivatives 1, 3, 4, 7, 8, 9, 11, 13, and 14 with increasing concentrations of E2 (from 0.01 pM to 1 nM) reduced both the potency and efficacy of pure agonists. The binding to the rhERα-LBD was validated by TR-FRET competitive binding assay and lignans bound to the rhERα with IC₅₀ values from 0.16 μM (compound 14) to 6 μM (compound 4). Induced fit docking (IFD) and molecular dynamics (MD) simulations for compound 14 were carried out to further investigate the binding mode interactions. Finally, the in silico ADME predictions indicated that the most potent lignan derivatives exhibited good drug-likeness.

Improvement of theoretical UV-Vis spectra calculations by empirical solvatochromic parameters: Case study of 5-arylazo-3-cyano-1-ethyl-6-hydroxy-4-methyl-2-pyridones

In order to improve the performance of theoretical UV-Vis spectra predictions, a theoretical and experimental study of solvatochromic properties of ten azo pyridone dyes has been performed. For quantitative estimation of intermolecular solvent-solute interactions, a concept of the linear solvation energy relationships has been applied using Kamlet-Taft and Catalán models. Theoretical UV-Vis spectra for all dyes have been calculated using four TD-DFT methods in nine different solvents with the aim to define the most reliable model. Finally, new polylinear equations for more accurate theoretical prediction of UV-Vis maxima are developed using empirical Kamlet-Taft and Catalán solvent parameters as additive corrections for specific and nonspecific solvent-solute interactions.