Prediction of intestinal permeability

Nanomolar activity of coumarin-3-thiosemicarbazones targeting Trypanosoma cruzi cruzain and the T. brucei cathepsin L-like protease

Trypanosoma cruzi (T. cruzi) and Trypanosoma brucei (T. brucei) urgently demand innovative drug development due to their impact on public health worldwide. Their cysteine proteases, Cruzain (CRZ) and the T. brucei Cathepsin L-like protease (TbrCATL) are established drug targets for these parasites. In this study, our coumarin-3-thiosemicarbazones demonstrated nanomolar IC50 values (22-698 nM) toward these proteases. Against T. cruzi amastigotes and T. brucei trypomastigotes, LASF-01 displayed a promising result. Herein, MCG-02, the most potent TbrCATL inhibitor, underwent comprehensive analyses, including cytotoxicity assessments and in vitro tests. Molecular dynamics (MD) simulations and a multiscale Quantum Mechanics/Quantum Mechanics (QM/QM) approach were used to generate insights into their binding modes. These suggested that MCG-02 could be a reversible, competitive covalent inhibitor. Further, confirmatory assays were experimentally performed changing different parameters to prove its efficacy. Additionally, the predicted pharmacokinetic profile showed that there is no violation of the Lipinski rule of five. Notably, coumarin-3-thiosemicarbazone hybrids emerged as promising candidates for designing highly active inhibitors against CRZ and TbrCATL. Overall, the integration of in silico and experimental approaches enhanced our understanding regarding the binding modes of MCG-02, which were experimentally corroborated, providing valuable insights for future drug development.

Developing multifaceted drug synergistic therapeutic strategy against neurological disorders

Drug synergism can alter the ultimate biological effects and bioavailability of phytoconstituents. Acetylcholinesterase (AChE) inhibitors as symptomatic drugs are potent therapeutic regimen for neurodegenerative diseases. In this context, this study characterized the synergistic antioxidant, anti-inflammatory and anti-AChE effects of the selected phytochemicals including standard drugs followed by enzyme kinetics, structure-based ligands screening and molecular dynamics simulation study. The synergistic interactions were evaluated through Isoradiation and Synergy finder 3.0 methods. The combinations of Quercetin (QCT), Folic acid (FA), and Swertiamarin (SWT) with specific reference drugs were studied. The combinations of SWT + GA (Gallic acid) and FA + GA at 1:1 (γ:0.10 & 0.08, respectively) showed the significant synergistic antioxidant effect via ABTS assay. Further, in combination, QCT + SWT showed the maximum synergistic effect (γ: 0.02-0.13) in anti-inflammatory assay. Moreover, the combinations QCT, FA, and SWT with reference drug, Donepezil (DP), illustrated potent synergistic activity as anti-AChE in 1:1 proportion (γ: 0.18). The interaction pattern of phytochemicals significantly exhibited synergism (γ < 1) depicting their optimum activity in combinations compared to individual components. Enzyme kinetics evaluation showed the competitive binding of SWT with AChE as of donepezil. All the parameters of ADMET study proposed the QCT and SWT as acceptable oral drug molecules. Computational docking study revealed that QCT and SWT with lowest RMSD (1.096, 2.104) and lowest docking score (-9.831, -7.435 kcal/mol) showed maximum binding efficacy. Furthermore, molecular simulation study depicted the stability of protein-ligand complexes. These findings provide novel insight in the development of dietary treatment based on their synergistic effects for neurological disorders as optimum alternative therapeutic agents.

Integrating (deep) machine learning and cheminformatics for predicting human intestinal absorption of small molecules

The oral route is the most preferred route for drug delivery, due to which the largest share of the pharmaceutical market is represented by oral drugs. Human intestinal absorption (HIA) is closely related to oral bioavailability making it an important factor in predicting drug absorption. In this study, we focus on predicting drug permeability at HIA as a marker for oral bioavailability. A set of 2648 compounds were collected from some early as well as recent works and curated to build a robust dataset. Five machine learning (ML) algorithms have been trained with a set of molecular descriptors of these compounds which have been selected after rigorous feature engineering. Additionally, two deep learning models - graph convolution neural network (GCNN) and graph attention network (GAT) based model were developed using the same set of compounds to exploit the predictability with automated extracted features. The numerical analyses show that out the five ML models, Random forest and LightGBM could predict with an accuracy of 87.71 % and 86.04 % on the test set and 81.43 % and 77.30 % with the external validation set respectively. Whereas with the GCNN and GAT based models, the final accuracy achieved was 77.69 % and 78.58 % on test set and 79.29 % and 79.42 % on the external validation set respectively. We believe deployment of these models for screening oral drugs can provide promising results and therefore deposited the dataset and models on the GitHub platform (https://github.com/hridoy69/HIA).

Modified Zhenwu Decoction improved intestinal barrier function of experimental colitis through activation of sGC-mediated cGMP/PKG signaling

BACKGROUND

The invasion of luminal antigens and an aberrant immune response resulting from a disrupted physical epithelial barrier are the key characteristics of ulcerative colitis (UC). The restoration of damaged epithelial function is crucial for maintaining mucosal homeostasis and disease quiescence. Current therapies for UC primarily focus on suppressing inflammation. However, most patients fail to respond to therapy or develop secondary resistance over time, emphasizing the need to develop novel therapeutic targets for UC. Our study aimed to identify the potential targets of a novel modified herbal formula from the Zhen Wu Decoction, namely CDD-2103, which has demonstrated promising efficacy in treating chronic colitis.

METHODS

The effect of CDD-2103 on epithelial barrier function was examined using in vitro and ex vivo models of tissue injury, as well as a chronic colitis C57BL/6 mouse model. Transcriptomic analysis was employed to profile gene expression changes in colonic tissues following treatment with CDD-2103.

RESULTS

Our in vivo experiments demonstrated that CDD-2103 dose-dependently reduced disease severity in mice with chronic colitis. The efficacy of CDD-2103 was mediated by a reduction in goblet cell loss and the enhancement of tight junction protein integrity. Mechanistically, CDD-2103 suppressed epithelial cell apoptosis and tight junction protein breakdown by activating the soluble guanynyl cyclase (sGC)-mediated cyclic guanosine monophosphate (cGMP)/PKG signaling cascade. Molecular docking analysis revealed strong sGC ligand recognition by the CDD-2103-derived molecules, warranting further investigation.

CONCLUSION

Our study revealed a novel formulation CDD-2103 that restores intestinal barrier function through the activation of sGC-regulated cGMP/PKG signaling. Furthermore, our findings suggest that targeting sGC can be an effective approach for promoting mucosal healing in the management of UC.

Synthesis and biological evaluation of novel aminoquinolines with an n-octyl linker: Impact of halogen substituents on C(7) or a terminal amino group on anticholinesterase and BACE1 activity

Alzheimer's disease is age-related multifactorial neurodegenerative disease manifested by gradual loss of memory, cognitive decline and changes in personality. Due to rapid and continuous growth of its prevalence, the treatment of Alzheimer's disease calls for development of new and efficacies drugs, especially those that could be able to simultaneously act on more than one of possible targets of action. Aminoquinolines have proven to be a highly promising structural scaffold in the design of such a drug as cholinesterases and β-secretase 1 inhibitors. In this study, we synthesised twenty-two new 4-aminoquinolines with different halogen atom and its position in the terminal N-benzyl group or with a trifluoromethyl or a chlorine as C(7)-substituents on the quinoline moiety. All compounds were evaluated as multi-target-directedligands by determining their inhibition potency towards human acetylcholinesterase, butyrylcholinesterase and β-secretase 1. All of the tested derivatives were very potent inhibitors of human acetylcholinesterase and butyrylcholinesterase with inhibition constants (Ki) in the nM to low μM range. Most were estimated to be able to cross the blood-brain barrier by passive transport and were nontoxic toward cells that represented the main models of individual organs.

Novel PPAR-γ agonists as potential neuroprotective agents against Alzheimer's disease: rational design, synthesis, in silico evaluation, PPAR-γ binding assay and transactivation and expression studies

Alzheimer's disease (AD) is a neurological disorder. It is caused by accumulation of amyloid beta (Aβ) plaques and tau tangles, which gradually leads to cognitive decline and memory loss. Peroxisome proliferator-activated receptor gamma (PPAR-γ), a nuclear receptor, plays a significant role in regulating genes responsible for metabolism and inflammation. Studies have shown that PPAR-γ activation has neuroprotective effects, can potentially reduce inflammation and oxidative stress, and stimulates mitochondrial biogenesis. Current study presents the design, synthesis and in vitro evaluation of PPAR-γ agonists for AD that are tailored to optimize binding with the PPAR-γ receptor. The compounds 4a, 4h and 4j exhibited notable binding affinities towards PPAR-γ LBD, with IC50 values of 8.607, 9.242, and 5.974 μM, respectively, in TR-FRET binding assay. These compounds were cell proliferative and non-cytotoxic in a neuroblastoma cell line (SH-SY5Y). They also demonstrated dose-dependent PPAR-γ activation in transactivation assay. Their neuroprotective effect was studied based on their anti-inflammatory and anti-oxidant potential by reducing the levels of proinflammatory markers (TNF-α, IL-6 and IL-1β) and ROS in Aβ-induced SH-SY5Y neuroblastoma cells using a flow cytometry method. The synthesized compounds also showed interactions in molecular docking study with the PPAR-γ receptor and demonstrated good stability in MD simulation. Our results highlight that through activation of PPAR-γ, the compounds 4a, 4h and 4j offer neuroprotective effects by reducing neuroinflammation and oxidative stress, and hence, they may be considered lead molecules for treating AD.

Identifying potential inhibitors of C-X-C motif chemokine ligand10 against vitiligo: structure-based virtual screening, molecular dynamics simulation, and principal component analysis

The research aims to envisage small molecule inhibitors targeting the C-X-C motif chemokine ligand 10 (CXCL10) of the JAK/STAT pathway. CXCL10 plays a significant role in inducing auto-immunity in vitiligo through JAK/STAT pathway. To accomplish the aim, structure-based virtual screening with fundamental search limits, e.g., molecular weight (MW ≤ 500 Da), hydrogen bond donor (HBD ≤ 5), hydrogen bond acceptor (HBA ≤ 10), and lipophilicity (logP ≤ 5) was used to screen investigational molecules from MCULE database. The SBVS-ligand hits were sifted through toxicity profiling followed by filtration through the Brain or IntestinaL EstimateD-Egg model to check the human intestinal abortion and blood-brain barrier permeation based on two physicochemical properties, including topological surface area and WLOGP. The BOILED-Egg filtered compounds were passed through drug-likeness features other than Pfizer's Lipinski rule of five, viz., Ghose filters, Muegge filters, Egan parameters, and Veber filters, followed by medicinal chemistry's pan assay interference structure and Brenk alert investigation. Chemical compounds that comply with the above ADME descriptors were docked with target protein CXCL10 via AutoDock Vina. The stability of the top two ligand hits was assessed through dynamics simulations of 100 ns and principal component analysis and compared with the reference drugs Baicalein and EGCG. Based on the findings of Gibbs free energy of binding, ADME profiling, medicinal chemistry attributes depiction, root-mean-square deviation, root-mean-square fluctuation, solvent accessible surface area, the free energy of solvation, the radius of gyration, and PCA, MCULE2726078782-0-2 was found better than potential reference drug Baicalein.Communicated by Ramaswamy H. Sarma.

In-vitro Evaluation of the Antifungal Property of Cold-Pressed Coconut oil Against Drug-Resistant Candida albicans and in-Silico Bioactivity Against Candidapepsin-2

Objective: This study focuses on Candida albicans, a significant fungal pathogen in humans, particularly affecting immunocompromised individuals and developing resistance to commonly used antifungal drugs. To address this challenge, the research assessed the in-vitro anti-candida properties of cold-pressed coconut oil. Additionally, the study conducted an in-silico evaluation of the oil's bioactive compounds against candidapepsin-2, an enzyme crucial in the virulence and pathogenesis of Candida infections. Materials and Methods: Extracted coconut oil was tested for its sterility and evaluated for its antifungal activity in-vitro using the agar well-diffusion methods with fluconazole as a positive control. Growth kinetics assay and synergism activity with fluconazole were also assessed. The coconut oil was quantitatively screened for its bioactive compounds using gas chromatography coupled to a mass spectrophotometer (GC-MS) and the resulting bioactive compounds were assessed for absorption, distribution, metabolism, excretion and toxicity (ADMET) properties using the SWISSADME tool. Compounds that met Lipinski's rule of five (ROF) were subjected to molecular docking against candidapepsin-2 using the Biovia (Discovery) docking tool. Results: The test isolates exhibited zones of inhibition ranging from 47–76 mm to the extract (100%) compared to 12–42 mm exhibited against fluconazole (400 mg) and 2–3 mm in plates containing only agar with MICs and MFCs ranging from 1.57–6.25% and 3.13 −12.5% against the extract compared to the control drug where MICs and MFCs of 6.25–12.5% and 12.5–25.0% were observed, respectively. The coconut extract exerted a concentration-dependent effect on the test isolates over time as higher extract concentrations decreased the optical density of cells to 0.001–0.06 at 72 h of incubation. Equal proportions of the extract + fluconazole exerted greater inhibitory potentials on the test isolates compared with those of low extract proportions. The synergistic-antagonistic antifungal assay showed enhanced sensitivity of the resistant isolates. Of the eleven (11) bioactive compounds quantitatively screened, only nine (9) met Lipinski's ROF and also returned favourable pharmacokinetics comparable to fluconazole. Docking scores for the bioactive compounds ranged from −2.0 to −3.0 kcal/mol. The most recurring amino acid residues following molecular docking were ILE and THR. Conclusion: The bioactive compounds showed desirable activities in-vitro, especially in synergy with fluconazole against the drug-resistant Candida species and in-silico and thus, require further studies to validate their potential use in the management of Candida-related infections.

An in-silico investigation based on molecular simulations of novel and potential brain-penetrant GluN2B NMDA receptor antagonists as anti-stroke therapeutic agents

GluN2B-induced activation of NMDA receptors plays a key function in central nervous system (CNS) disorders, including Parkinson, Alzheimer, and stroke, as it is strongly involved in excitotoxicity, which makes selective NMDA receptor antagonists one of the potential therapeutic agents for the treatment of neurodegenerative diseases, especially stroke. The present study aims to examine a structural family of thirty brain-penetrating GluN2B N-methyl-D-aspartate (NMDA) receptor antagonists, using virtual computer-assisted drug design (CADD) to discover highly candidate drugs for ischemic strokes. Initially, the physicochemical and ADMET pharmacokinetic properties confirmed that C13 and C22 compounds were predicted as non-toxic inhibitors of CYP2D6 and CYP3A4 cytochromes, with human intestinal absorption (HIA) exceeding 90%, and designed to be as efficient central nervous system (CNS) agents due to the highest probability to cross the blood-brain barrier (BBB). Compared to ifenprodil, a co-crystallized ligand complexed with the transport protein encoded as 3QEL.pdb, we have noticed that C13 and C22 chemical compounds were defined by good ADME-Toxicity profiles, meeting Lipinski, Veber, Egan, Ghose, and Muegge rules. The molecular docking results indicated that C22 and C13 ligands react specifically with the amino acid residues of the NMDA receptor subunit GluN1 and GluN2B. These intermolecular interactions produced between the candidate drugs and the targeted protein in the B chain remain stable over 200 nanoseconds of molecular dynamics simulation time. In conclusion, C22 and C13 ligands are highly recommended as anti-stroke therapeutic drugs due to their safety and molecular stability towards NMDA receptors.Communicated by Ramaswamy H. Sarma.

Structural exploration of the PfBLM Helicase-ATP Binding Domain and implications in the quest for antimalarial therapies

BACKGROUND OBJECTIVES

The battle against malaria has witnessed remarkable progress in recent years, characterized by increased funding, development of life-saving tools, and a significant reduction in disease prevalence. Yet, the formidable challenge of drug resistance persists, threatening to undo these gains.

METHODS

To tackle this issue, it is imperative to identify new effective drug candidates against the malaria parasite that exhibit minimal toxicity. This study focuses on discovering such candidates by targeting PfRecQ1, also known as PfBLM, a vital protein within the malaria parasite Plasmodium falciparum . PfRecQ1 plays a crucial role in the parasite's life cycle and DNA repair processes, making it an attractive drug development target. The study employs advanced computational techniques, including molecular modeling, structure-based virtual screening (SBVS), ADMET profiling, molecular docking, and dynamic simulations.

RESULTS

The study sources ligand molecules from the extensive MCULE database and utilizes strict filters to ensure that the compounds meet essential criteria. Through these techniques, the research identifies MCULE-3763806507-0-9 as a promising antimalarial drug candidate, surpassing the binding affinity of potential antimalarial drugs. However, it is essential to underscore that drug-like properties are primarily based on in silico experiments, and wet lab experiments are necessary to validate these candidates' therapeutic potential.

INTERPRETATION CONCLUSION

This study represents a critical step in addressing the challenge of drug resistance in the fight against malaria.

Evaluation of Anticholinesterase Activity of the Fungicides Mefentrifluconazole and Pyraclostrobin

Triazoles are compounds with various biological activities, including fungicidal action. They became popular through cholinesterase studies after the successful synthesis of the dual binding femtomolar triazole inhibitor of acetylcholinesterase (AChE, EC 3.1.1.7) by Sharpless et al. via in situ click chemistry. Here, we evaluate the anticholinesterase effect of the first isopropanol triazole fungicide mefentrifluconazole (Ravystar®), developed to overcome fungus resistance in plant disease management. Mefentrifluconazole is commercially available individually or in a binary fungicidal mixture, i.e., with pyraclostrobin (Ravycare®). Pyraclostrobin is a carbamate that contains a pyrazole ring. Carbamates are known inhibitors of cholinesterases and the carbamate rivastigmine is already in use for the treatment of Alzheimer's disease. We tested the type and potency of anticholinesterase activity of mefentrifluconazole and pyraclostrobin. Mefentrifluconazole reversibly inhibited human AChE and BChE with a seven-fold higher potency toward AChE (Ki = 101 ± 19 μM). Pyraclostrobin (50 μM) inhibited AChE and BChE progressively with rate constants of (t1/2 = 2.1 min; ki = 6.6 × 103 M-1 min-1) and (t1/2 = 1.5 min; ki = 9.2 × 103 M-1 min-1), respectively. A molecular docking study indicated key interactions between the tested fungicides and residues of the lipophilic active site of AChE and BChE. Additionally, the physicochemical properties of the tested fungicides were compared to values for CNS-active drugs to estimate the blood-brain barrier permeability. Our results can be applied in the design of new molecules with a lesser impact on humans and the environment.

Design, synthesis and biological evaluation of 1-aryldonepezil analogues as anti-Alzheimer's disease agents

Aim: To design and synthesize a novel series of 1-aryldonepezil analogues. Materials & methods: The 1-aryldonepezil analogues were synthesized through palladium/PCy3-catalyzed Suzuki reaction and were evaluated for cholinesterase inhibitory activities and neuroprotective effects. In silico docking of the most effective compound was conducted. Results: The 4-tert-butylphenyl analogue exhibited good inhibitory potency against acetylcholinesterase and butyrylcholinesterase and had a favorable neuroprotective effect on H2O2-induced SH-SY5Y cell injury. Conclusion: The 4-tert-butylphenyl derivative is a promising lead compound for anti-Alzheimer's disease drug development.

A novel angiotensin I-converting enzyme inhibitory peptide from walnut (Juglans sigillata) protein hydrolysates and its evaluation in Ang II-induced HUVECs and hypertensive rats

This study aims to seek angiotensin-I-converting enzyme inhibitory (ACEi) peptides from walnut using different enzymatic hydrolysis, and further to validate the potent ACEi peptides identified and screened via peptidomics and in silico analysis against hypertension in spontaneously hypertensive rats (SHRs). Results showed that walnut protein hydrolysate (WPH) prepared by combination of alcalase and simulated gastrointestinal digestion exhibited high ACEi activity. WPH was separated via Sephadex-G25, and four peptides were identified, screened and verified based on their PeptideRanker score, structural characteristic and ACE inhibition. Interestingly, FDWLR showed the highest ACEi activity with IC50 value of 8.02 μg/mL, which might be related to its close affinity with ACE observed in molecular docking. Subsequently, high absorption and non-toxicity of FDWLR was predicted via in silico absorption, distribution, metabolism, excretion and toxicity. Furthermore, FDWLR exhibited positively vasoregulation in Ang II-induced human umbilical vein endothelial cells, and great blood pressure lowering effect in SHRs.

Environmentally benign synthesis of unsymmetrical ureas and their evaluation as potential HIV-1 protease inhibitors via a computational approach

The present work reports the cost-effective, high yielding and environmentally acceptable preparation of unsymmetrical ureas from thiocarbamate salts using sodium percarbonate as an oxidant. Efficacy of the unsymmetrical ureas as potential human immune deficiency virus (HIV-1) protease inhibitors has been evaluated via in silico approach. The results revealed interactions of the urea compounds at the active site of the enzyme with favorable binding affinities causing possible mutations hindering the functioning of the enzyme. Further computational assessment of IC50 using known references satisfactorily authenticated the inhibitory action of the selected compounds against HIV-1 protease. Added to the easy synthesis of the ureas following an environmentally benign protocol, this work may be a valuable addition to the ongoing search for drugs with better efficacy profiles and reduced toxicity against HIV.

Enhanced Calculation of Property Distributions in Chemical Fragment Spaces

Chemical fragment spaces exceed traditional virtual compound libraries by orders of magnitude, making them ideal search spaces for drug design projects. However, due to their immense size, they are not compatible with traditional analysis and search algorithms that rely on the enumeration of molecules. In this paper, we present SpaceProp2, an evolution of the SpaceProp algorithm, which enables the calculation of exact property distributions for chemical fragment spaces without enumerating them. We extend the original algorithm by the capabilities to compute distributions for the TPSA, the number of rotatable bonds, and the occurrence of user-defined molecular structures in the form of SMARTS patterns. Furthermore, SpaceProp2 produces example molecules for every property bin, enabling a detailed interpretation of the distributions. We demonstrate SpaceProp2 on six established make-on-demand chemical fragment spaces as well as BICLAIM, the in-house fragment space of Boehringer Ingelheim. The possibility to search multiple SMARTS patterns simultaneously as well as the produced example molecules offers previously impossible insights into the composition of these vast combinatorial molecule collections, making it an ideal tool for the analysis and design of chemical fragment spaces.

Molecular interactions of paraben family of pollutants with embryonic neuronal proteins of Danio rerio: A step ahead in computational toxicity towards adverse outcome pathway

The paraben family of endocrine disruptors exhibit persistent behaviours in aquatic matrices, having bio-accumulative effects and necessitating toxicity analysis and safe use, as well as prevention of food web penetration. In this study, the toxicity effects of 9 different parabens (Methyl, Ethyl, Propyl, Butyl, Heptyl, Isopropyl, Isobutyl, benzyl parabens and p-hydroxybenzoic acid) were studied against 17 neuronal proteins (Neurog1, Ascl1a, DLA, Syn2a, Ntn1a, Pitx2, and SoxB1, Her/Hes, Zic family) expressed during the early embryonic developmental stage of Danio rerio. The neuronal genes were selected as a biomarker to study the inhibitory effects on the cascade of genes expressed in the early developmental stage. The study uses trRossetta software to predict protein structures of neuronal genes, followed by structural refinement, energy minimisation, and active site prediction, evaluated using energy value, RC plot and ERRAT scores of PROCHECK and ERRAT programs. Compared to raw structures, highly confident predicted structures and quality scores were observed for refined protein with few exceptions. Based on the polarity and charge of the aminoacids, the probable pockets were identified using active site prediction, which were then used for molecular docking analysis. Further, the ADMET analysis, ligand likeliness and toxicological test revealed the paraben family of compounds as one of the most susceptible toxic and mutagenic compounds. The molecular docking results showed an interesting pattern of increasing binding affinity with increase in the carbon chains of paraben molecules. Benzyl Paraben showed higher binding affinities across all 17 neuronal proteins. Finally, gene co-occurrence/co-expression and protein-protein interaction studies using the STRING database depict that all proteins are functionally related and play essential roles in standard biological processes or pathways, conserved and expressed in diverse organisms. The interaction between paraben compounds and neuronal genes indicates high risks of inhibiting reactions in embryonic stages, emphasising the need for effective treatment measures and strict regulations.

Impact of the Unstirred Water Layer on the Permeation of Small-Molecule Drugs

Over the last two decades, numerous molecular dynamics (MD) simulation-based investigations have attempted to predict the membrane permeability to small-molecule drugs as indicators of their bioavailability, a majority of which utilize the inhomogeneous solubility diffusion (ISD) model. However, MD-based membrane permeability is routinely 3-4 orders of magnitude larger than the values measured with the intestinal perfusion technique. There have been contentious discussions on the sources of the large discrepancies, and the two indisputable, potentially dominant ones are the fixed protonation state of the permeant and the neglect of the unstirred water layer (UWL). Employing six small-molecule drugs of different biopharmaceutical classification system classes, the current MD study relies on the ISD model but introduces the (de)protonation of the permeant by characterizing the permeation free energy of both neutral and charged states. In addition, the role of the UWL as a potential resistance against permeation is explored. The new MD protocol closely mimics the nature of small-molecule permeation and yields estimates that agree well with in vivo intestinal permeability.

In Silico Study in MPO and Molecular Docking of the Synthetic Drynaran Analogues Against the Chronic Tinnitus: Modulation of the M1 Muscarinic Acetylcholine Receptor

Tinnitus is a syndrome that affects the human auditory system and is characterized by a perception of sounds in the absence of acoustic stimuli, or in total silence. Research indicates that muscarinic acetylcholine receptors (mAChRs), especially the M1 type, have a fundamental role in the alterations of auditory perceptions of tinnitus. Here, a series of computer-aided tools were used, from molecular surface analysis software to services available on the web for estimating pharmacokinetics and pharmacodynamics. The results infer that the low lipophilicity ligands, that is, the 1a-d alkyl furans, present the best pharmacokinetic profile, as compounds with an optimal alignment between permeability and clearance. However, only ligands 1a and 1b have properties that are safe for the central nervous system, the site of cholinergic modulation. These ligands showed similarity with compounds deposited in the European Molecular Biology Laboratory chemical (ChEMBL) database acting on the mAChRs M1 type, the target selected for the molecular docking test. The simulations suggest that the 1 g ligand can form the ligand-receptor complex with the best affinity energy order and that, together with the 1b ligand, they are competitive agonists in relation to the antagonist Tiotropium, in addition to acting in synergism with the drug Bromazepam in the treatment of chronic tinnitus.

Improving ADMET Prediction Accuracy for Candidate Drugs: Factors to Consider in QSPR Modeling Approaches

Quantitative Structure-Property Relationship (QSPR) employs mathematical and statistical methods to reveal quantitative correlations between the pharmacokinetics of compounds and their molecular structures, as well as their physical and chemical properties. QSPR models have been widely applied in the prediction of drug absorption, distribution, metabolism, excretion, and toxicity (ADMET). However, the accuracy of QSPR models for predicting drug ADMET properties still needs improvement. Therefore, this paper comprehensively reviews the tools employed in various stages of QSPR predictions for drug ADMET. It summarizes commonly used approaches to building QSPR models, systematically analyzing the advantages and limitations of each modeling method to ensure their judicious application. We provide an overview of recent advancements in the application of QSPR models for predicting drug ADMET properties. Furthermore, this review explores the inherent challenges in QSPR modeling while also proposing a range of considerations aimed at enhancing model prediction accuracy. The objective is to enhance the predictive capabilities of QSPR models in the field of drug development and provide valuable reference and guidance for researchers in this domain.

3D-QSAR and ADMET studies of morpholino-pyrimidine inhibitors of DprE1 from Mycobacterium tuberculosis

DprE1 is involved in the synthesis of Mycobacterium tuberculosis cell wall and is a potent drug target for Tuberculosis (TB) treatment. The structure and dynamics of the loops L-I and L-II flanking the inhibitor binding site was studied using molecular dynamics (MD) simulation and MMPBSA in Amber v18. Docking and three-dimensional quantitative structure-activity relationship (3D-QSAR) of 55 Morpholino-pyrimidine (MP) inhibitors was carried out using Autodock v1.2.0 and Forge v10. ADMET analysis was done using SwissADME and pkCSM. All MP inhibitors docked in the DprE1 binding pocket, making contacts with L-II residues. MD studies showed that L-I and L-II unfold in the absence of the inhibitor but fold stably structure with reduced protein motions in the presence of MP-38, the highest affinity inhibitor. This was confirmed by k-means clustering and secondary structure analysis. L-II residues, L317, F320 and R325 contributed most towards the MMPBSA binding free energy of MP-38. A robust field-based 3D-QSAR model showed values of r2train = 0.982, r2test = 0.702 and q2 = 0.516. The MP inhibitor field points were broadly divided into negative electrostatics near the A, B rings and hydrophobic electrostatics near the D, E rings. Addition of negative groups at methanone position and ring B as well as addition of hydrophobic and bulky groups at ring E will improve activity. Highly active compounds 47, 49 and 50 of MP series exhibited highly favourable drug-like properties. SAR and ADMET insights attained from this model will help in the development of active DprE1 inhibitors in future.Communicated by Ramaswamy H. Sarma.

Preclinical data on morpholine (3,5-di-tertbutyl-4-hydroxyphenyl) methanone induced anxiolysis

Trimetozine is used to be indicated for the treatment of mental illnesses, particularly anxiety. The present study provides data on the pharmacological profile of trimetozine derivative morpholine (3,5-di-tert-butyl-4-hydroxyphenyl) methanone (LQFM289) which was designed from molecular hybridization of trimetozine lead compound and 2,6-di-tert-butyl-hydroxytoluene to develop new anxiolytic drugs. Here, we conduct molecular dynamics simulations, docking studies, receptor binding assays, and in silico ADMET profiling of LQFM289 before its behavioral and biochemical assessment in mice within the dose range of 5-20 mg/kg. The docking of LQFM289 showed strong interactions with the benzodiazepine binding sites and matched well with receptor binding data. With the ADMET profile of this trimetozine derivative that predicts a high intestinal absorption and permeability to blood-brain barrier without being inhibited by the permeability glycoprotein, the oral administration of LQFM289 10 mg/kg consistently induced anxiolytic-like behavior of the mice exposed to the open field and light-dark box apparatus without eliciting motor incoordination in the wire, rotarod, and chimney tests. A decrease in the wire and rotarod´s fall latency coupled with an increase in the chimney test´s climbing time and a decrease in the number of crossings in the open field apparatus at the dose of 20 mg/kg of this trimetozine derivative suggest sedative or motor coordination impairment at this highest dose. The attenuation of the anxiolytic-like effects of LQFM289 (10 mg/kg) by flumazenil pretreatment implicates the participation of benzodiazepine binding sites. The lowering of corticosterone and tumor necrosis factor alpha (cytokine) in LQFM289-treated mice at a single oral (acute) dose of 10 mg/kg suggests that the anxiolytic-like effect of this compound also involves the recruitment of non-benzodiazepine binding sites/GABAergic molecular machinery.

Purification and structure elucidation of Penicillium chrysogenum derived antifungal compound with potential anti-Candida property: in silico and in vitro evidence

Following preliminary bioactivity testing, the fungal strain identified as Penicillium crysogenum was cultured in a modified Czapec Yeast Broth medium (CYB) for the production of antifungal compounds. Several chromatographic techniques including HPLC were used to purify the fungal metabolites from the crude extract. The mass determination of the purified compound was performed using Water's LCMS system while the structure of the compound was elucidated using 400 and 500 Varian NMR machines. The chemical name of the purified compound is (2 R, 4S) -2, 4-dimethyl-4-((E)-2-((3S, 4S)-2, 4, 5-trihydroxy-3-methoxy-4-phenyl-1, 2, 3, 4-tetrahydroquinolin-6-yl) vinyl) cyclohexanone with the chemical formula C26H31NO5 and exact mass of 437.2. Molecular docking predicted compound docking score with dihydrofolate reductase enzyme and lanosterol 14α-demethylase enzyme as -8.1 kcal/mol and -9.8 kcal/mol respectively. Further, the compounds showed stable binding mode with the enzymes and reported robust binding energies. After insilico analysis, the compound with mass 437 was tested for its antifungal potential in vitro against two pathogenic yeast species (i.e. Candida albicans and Candida glaberata) using the agar tube diffusion method. Using sterile di-methyl sulfoxide (DMSO) the compound was prepared in four dose concentrations (100, 250, 500, 1000 µg mL-1) and mixed with autoclaved semisolid Potato Dextrose Agar (PDA) medium in screw-capped test tubes labelled with the corresponding dose concentration. The fungal strains were inoculated on this medium and linear growth inhibition of the fungal strains was calculated using fluconazole as the control drug. The results from in vitro experiments were encouraging as at concentrations of 500 and 1000 μg mL-1 the compound inhibited the growth of C. albicans by 17% and 38% while 19% and 41% inhibition were recorded against C. glaberata. The compound showed antifungal activity in silico and in vitro against both the Candida species and can act as a potent antifungal candidate in the future upon further investigation.Communicated by Ramaswamy H. Sarma.

In-silico and in-vitro study reveals ziprasidone as a potential aromatase inhibitor against breast carcinoma

Aromatase enzyme plays a fundamental role in the development of estrogen receptors, and due to this functionality, the enzyme has gained significant attention as a therapeutic for reproductive disorders and cancer diseases. The currently employed aromatase inhibitors have severe side effects whereas our novel aromatase inhibitor is more selective and less toxic, therefore has greater potential to be developed as a drug. The research framework of this study is to identify a potent inhibitor for the aromatase target by profiling molecular descriptors of the ligand and to find a functional pocket in the target by docking and MD simulations. For assessing cellular and metabolic activities as indicators of cell viability and cytotoxicity, in-vitro studies were performed by using the colorimetric MTT assay. Aromatase activities were determined by a fluorometric method. Cell morphology was assessed by phase-contrast light microscopy. Flow cytometry and Annexin V-FITC/PI staining assay determined cell cycle distribution and apoptosis. This study reports that CHEMBL708 (Ziprasidone) is the most promising compound that showed excellent aromatase inhibitory activity. By using better drug design methods and experimental studies, our study identified a novel compound that could be effective as a high-potential drug candidate against aromatase enzyme. We conclude that the compound ziprasidone effectively blocks the cell cycle at the G1-S phase and induces cancer cell death. Further, in-vivo studies are vital for developing ziprasidone as an anticancer agent. Lastly, our research outcomes based on the results of the in-silico experiments may pave the way for identifying effective drug candidates for therapeutic use in breast cancer.

Synthesis, characterization and evaluation of prenylated chalcones ethers as promising antileishmanial compounds

Drug therapy for leishmaniasis remains a major challenge as currently available drugs have limited efficacy, induce serious side-effects and are not accessible to everyone. Thus, the discovery of affordable drugs is urgently needed. Chalcones present a great potential as bioactive agents due to simple structure and functionalization capacity. The antileishmanial activity of different natural and synthetic chalcones have been reported. Here we report the synthesis of twenty-five novel prenylated chalcones that displayed antiparasitic activity in Leishmania mexicana. All the chalcones were evaluated at 5 µg/mL and eleven compounds exhibited a metabolic inhibition close to or exceeding 50%. Compounds 49, 30 and 55 were the three most active with IC50 values < 10 μM. These chalcones also showed the highest selectivity index (SI) values. Interestingly 49 and 55 possessing a substituent at a meta position in the B ring suggests that the substitution pattern influences antileishmanial activity. Additionally, a tridimensional model of fumarate reductase of L. mexicana was obtained by homology modeling. Docking studies suggest that prenylated chalcones could modulate fumarate reductase activity by binding with good affinity to two binding sites that are critical for the target. In conclusion, the novel prenylated chalcones could be considered as promising antileishmanial agents.

Design and Synthesis of Novel 5-((3-(Trifluoromethyl)piperidin-1-yl)sulfonyl)indoline-2,3-dione Derivatives as Promising Antiviral Agents: In Vitro, In Silico, and Structure-Activity Relationship Studies

Herein, a series of new isatin derivatives was designed and synthesized (1-9) as broad-spectrum antiviral agents. Consequently, the antiviral activities of the synthesized compounds (1-9) were pursued against three viruses, namely influenza virus (H1N1), herpes simplex virus 1 (HSV-1), and coxsackievirus B3 (COX-B3). In particular, compounds 9, 5, and 4 displayed the highest antiviral activity against H1N1, HSV-1, and COX-B3 with IC50 values of 0.0027, 0.0022, and 0.0092 µM, respectively. Compound 7 was the safest, with a CC50 value of 315,578.68 µM. Moreover, a quantitative PCR (real-time PCR) assay was carried out for the most relevant compounds. The selected compounds exhibited a decrease in viral gene expression. Additionally, the conducted in silico studies emphasized the binding affinities of the synthesized compounds and their reliable pharmacokinetic properties as well. Finally, a structure-antiviral activity relationship study was conducted to anticipate the antiviral activity change upon future structural modification.

Evaluation of 4-aminoquinoline derivatives with an n-octylamino spacer as potential multi-targeting ligands for the treatment of Alzheimer's disease

The most successful therapeutic strategy in the treatment of Alzheimer's disease (AD) is directed toward increasing levels of the neurotransmitter acetylcholine (ACh) by inhibition of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), the enzymes responsible for its hydrolysis. In this paper, we extended our study on 4-aminoquinolines as human cholinesterase inhibitors on twenty-six new 4-aminoquinolines containing an n-octylamino spacer on C(4) and different substituents on the terminal amino group. We evaluated the potency of new derivatives to act as multi-targeted ligands by determining their inhibition potency towards human AChE and BChE, ability to chelate biometals Fe, Cu and Zn, ability to inhibit the action of β-secretase 1 (BACE1) and their antioxidant capacity. All of the tested derivatives were very potent inhibitors of human AChE and BChE with inhibition constants (Ki) ranging from 0.0023 to 1.6 μM. Most of the compounds were estimated to be able to cross the blood-brain barrier (BBB) by passive transport and were nontoxic to human neuronal, kidney and liver cells in concentrations in which they inhibit cholinesterases. Generally, newly synthesised compounds were weak reductants compared to standard antioxidants, but all possessed a certain amount of antioxidant activity compared to tacrine. Of the eleven most potent cholinesterase inhibitors, eight compounds also inhibited BACE1 activity at 10-18%. Based on our overall results, compounds 8 with 3-fluorobenzyl, 11 with 3-chlorobenzyl and 17 with 3-metoxy benzyl substituents on the terminal amino group stood out as the most promising for the treatment of AD; they strongly inhibited AChE and BChE, were non-toxic on HepG2, HEK293 and SH-SY5Y cells, had the potential to cross the BBB and possessed the ability to chelate biometals and/or inhibit the activity of BACE1 within a range close to the therapeutically desired degree of inhibition.

Antimicrobial analysis of honey against Staphylococcus aureus isolates from wound, ADMET properties of its bioactive compounds and in-silico evaluation against dihydropteroate synthase

BACKGROUND

One of the main challenges of wound healing is infection with multi-drug resistant (MDR) bacteria such as Staphylococcus aureus. The spectrum of antibiotics used to treat them is declining; thus, there is a need for alternatives. Our study was designed to evaluate the antimicrobial properties of honey, its pharmacokinetics (ADMET) properties and in-silico analysis of its bioactive compounds against dihydropteroate synthase of S. aureus using trimethoprim as control.

METHODS

Standard protocols were employed in collection and preparation of samples, generation of canonical strings, and conduction of microbiological analyses. Bioactive compounds' ADMET properties were evaluated using the SWISSADME and the MCULE toxicity checker tools. The MCULE one-click docking tool was used in carrying out the dockings.

RESULTS

The gas chromatography-mass spectrophotometry revealed twenty (20) bioactive compounds and was dominated by sugars (> 60%). We isolated a total of 47 S. aureus isolates from the wound samples. At lower concentrations, resistance to trimethoprim (95.74 to 100.00%) was higher than honey (70.21 to 96.36%). Only seven (7) isolates meet Lipinski's rule of five and ADMET properties. The docking scores of the bioactive compounds ranged from -3.3 to -4.6 while that of trimethoprim was -6.1, indicating better binding or interaction with the dihydropteroate synthase. The bioactive compounds were not substrates to P450 cytochrome enzymes (CYP1A2, CYP2CI9 and CYP2D6) and p-glycoprotein, indicating better gastrointestinal tract (GIT) absorption.

CONCLUSION

The favourable docking properties shown by the bioactive compounds suggest they could be lead compounds for newer antimetabolites for management of MDR S. aureus.

QSAR, ADME-Tox, molecular docking and molecular dynamics simulations of novel selective glycine transporter type 1 inhibitors with memory enhancing properties

A structural class of forty glycine transporter type 1 (GlyT1) inhibitors, was examined using molecular modeling techniques. The quantitative structure-activity relationships (QSAR) technology confirmed that human GlyT1 activity is strongly and significantly affected by constitutional, geometrical, physicochemical and topological descriptors. ADME-Tox in-silico pharmacokinetics revealed that L28 and L30 ligands were predicted as non-toxic inhibitors with a good ADME profile and the highest probability to penetrate the central nervous system (CNS). Molecular docking results indicated that the predicted inhibitors block GlyT1, reacting specifically with Phe319, Phe325, Tyr123, Tyr 124, Arg52, Asp475, Ala117, Ala479, Ile116 and Ile483 amino acids of the dopamine transporter (DAT) membrane protein. These results were qualified and strengthened using molecular dynamics (MD) study, which affirmed that the established intermolecular interactions for (L28, L30-DAT protein) complexes remain perfectly stable along 50 ns of MD simulation time. Therefore, they could be strongly recommended as therapeutics in medicine to improve memory performance.

Screening and identification of potential MERS-CoV papain-like protease (PLpro) inhibitors; Steady-state kinetic and Molecular dynamic studies

MERS-CoV belongs to the coronavirus group. Recent years have seen a rash of coronavirus epidemics. In June 2012, MERS-CoV was discovered in the Kingdom of Saudi Arabia, with 2,591 MERSA cases confirmed by lab tests by the end of August 2022 and 894 deaths at a case-fatality ratio (CFR) of 34.5% documented worldwide. Saudi Arabia reported the majority of these cases, with 2,184 cases and 813 deaths (CFR: 37.2%), necessitating a thorough understanding of the molecular machinery of MERS-CoV. To develop antiviral medicines, illustrative investigation of the protein in coronavirus subunits are required to increase our understanding of the subject. In this study, recombinant expression and purification of MERS-CoV (PLpro), a primary goal for the development of 22 new inhibitors, were completed using a high throughput screening methodology that employed fragment-based libraries in conjunction with structure-based virtual screening. Compounds 2, 7, and 20, showed significant biological activity. Moreover, a docking analysis revealed that the three compounds had favorable binding mood and binding free energy. Molecular dynamic simulation demonstrated the stability of compound 2 (2-((Benzimidazol-2-yl) thio)-1-arylethan-1-ones) the strongest inhibitory activity against the PLpro enzyme. In addition, disubstitutions at the meta and para locations are the only substitutions that may boost the inhibitory action against PLpro. Compound 2 was chosen as a MERS-CoV PLpro inhibitor after passing absorption, distribution, metabolism, and excretion studies; however, further investigations are required.

Exposure to high-performance benzotriazole ultraviolet stabilizers: Advance in toxicological effects, environmental behaviors and remediation mechanism using in-silica methods

Benzotriazole ultraviolet stabilizers (BUVSs), as light stabilizers, have attracted widespread attention because of their easy migration in the environment and their acute toxicity and biological toxicity effects, such as immunotoxicity and hepatotoxicity. Accordingly, the treatment and remediation mechanisms of high-performance, environmentally friendly, and low human health risk BUVS substitutes were analyzed. Firstly, the weights and the comprehensive effect (CE) values of migration and toxicity of BUVSs were determined by Topsis assisted by the coefficient of variation (CV) method. From this, a three-dimensional quantitative structure activity relationship (3D-QSAR) model based on the CE values of the 13 BUVSs was constructed. Secondly, EPI software was used to predict the functionality and environmental friendliness of BUVS substitutes, and a partial least squares regression machine learning (ML-PLSR) model was used to analyze the mechanism. Then, ADMET (absorption, distribution, metabolism, excretion, toxicity), TOPKAT, and exposure dose models were used to evaluate the ecological and human health risks of BUVSs and their substitutes. Finally, the key charge information affecting the UV-326 substitutes was deduced by time dependent density functional theory (TDDFT). Using UV-326 as an example, 15 UV-326 substitutes with reduced CE values were designed (reductions of 2.61%-23.18%). Compared with ML-PLSR models of acute toxicity, immunotoxicity, and hepatotoxicity, it was found that the decrease of DM and Q_yy values and the increase of Q_zz value could further decrease the toxicity of the UV-326 substitutes. Ecological and human health risk assessment showed that the exposure risks of the six UV-326 substitutes were within acceptable limits. TDDFT showed that the change of electron distribution and electron excitation type were the key factors affecting the performance of the UV-326 substitutes, and a charge transfer excitation type was more conducive to obtaining high-performance, environmentally friendly UV-326 substitutes. This study aims to alleviate the toxic damage to the ecological environment and human health caused by BUVS exposure.

Selene-Ethylenelacticamides and N-Aryl-Propanamides as Broad-Spectrum Leishmanicidal Agents

The World Health Organization classifies Leishmania as one of the 17 “neglected diseases” that burden tropical and sub-tropical climate regions with over half a million diagnosed cases each year. Despite this, currently available anti-leishmania drugs have high toxicity and the potential to be made obsolete by parasite drug resistance. We chose to analyze organoselenides for leishmanicidal potential given the reduced toxicity inherent to selenium and the displayed biological activity of organoselenides against Leishmania. Thus, the biological activities of 77 selenoesters and their N-aryl-propanamide derivatives were predicted using robust in silico models of Leishmania infantum, Leishmania amazonensis, Leishmania major, and Leishmania (Viannia) braziliensis. The models identified 28 compounds with >60% probability of demonstrating leishmanicidal activity against L. infantum, and likewise, 26 for L. amazonesis, 25 for L. braziliensis, and 23 for L. major. The in silico prediction of ADMET properties suggests high rates of oral absorption and good bioavailability for these compounds. In the in silico toxicity evaluation, only seven compounds showed signs of toxicity in up to one or two parameters. The methodology was corroborated with the ensuing experimental validation, which evaluated the inhibition of the Promastigote form of the Leishmania species under study. The activity of the molecules was determined by the IC50 value (µM); IC50 values < 20 µM indicated better inhibition profiles. Sixteen compounds were synthesized and tested for their activity. Eight molecules presented IC50 values < 20 µM for at least one of the Leishmania species under study, with compound NC34 presenting the strongest parasite inhibition profile. Furthermore, the methodology used was effective, as many of the compounds with the highest probability of activity were confirmed by the in vitro tests performed.

Novel fluorinated pyrazole-based heterocycles scaffold: cytotoxicity, in silico studies and molecular modelling targeting double mutant EGFR L858R/T790M as antiproliferative and apoptotic agents

Hepatocellular carcinoma (HCC), also known as hepatoma, is the most prevalent type of primary liver cancer. It begins in the hepatocytes, the liver’s major cell type. Cancer that began in another region of the body but has spread to the liver is known as secondary cancer of life; several still unmet demands for better, less toxic therapy to treat this malignant tumor. Several novel pyrazolo[1,5-a]pyrimidine derivatives were synthesized as part of our goal to develop promising anticancer drugs. All the synthesized hybrids have been screened for their cytotoxicity effect against three cancer cell lines which are; HepG-2, HCT-116, and MCF-7. The liver cancer cells were found to be the most sensitive to the effect of the new molecules. A subsequent set of in vitro biological evaluation studies has been conducted on the most promising derivatives to identify their effect on such a cancer type. In HepG-2 cells, four derivatives (8a, 8b, 10c, and 11b) demonstrated good anticancer activity. The most efficacious compounds were 8b and 10c, which had IC50 values of 2.36 ± 0.14 and 1.14 ± 0.063 μM, respectively, higher than the reference medication Imatinib. The latter’s putative molecular effect has been investigated further by looking at its influence on the cell cycle, EGFR, and specific apoptotic and anti-apoptotic markers in HepG-2 cells. These findings indicated that 8b and 10c could trigger apoptosis by upregulating BAX and caspase-3 and cell cycle at the Pre-G1 and G2-M stages. The compounds 8b and 10c showed high potency for EGFR with IC50 equal to 0.098 and 0.079 μM, respectively. Compound 10c had the most effective inhibitory activity for EGFR L858R-TK with IC50 (36.79 nM). Additionally, in silico ADMET and docking studies were done for the most active hits, representing good results.

Graphical Abstract

Structure based design and synthesis of 3-(7-nitro-3-oxo-3,4-dihydroquinoxalin-2-yl)propanehydrazide derivatives as novel bacterial DNA-gyrase inhibitors: In-vitro, In-vivo, In-silico and SAR studies

Antimicrobial resistance (AMR) is one of the critical challenges that have been encountered over the past years. On the other hand, bacterial DNA gyrase is regarded as one of the most outstanding biological targets that quinolones can extensively inhibit, improving AMR. Hence, a novel series of 3-(7-nitro-3-oxo-3,4-dihydroquinoxalin-2-yl)propanehydrazide derivatives (3-6j) were designed and synthesized employing the quinoxaline-2-one scaffold and relying on the pharmacophoric features experienced by the quinolone antibiotic; ciprofloxacin. The antibacterial activity of the synthesized compounds was assessed via in-vitro approaches using eight different Gram-positive and Gram-negative bacterial species. Most of the synthesized compounds revealed eligible antibacterial activities. In particular, compounds 6d and 6e displayed promising antibacterial activity among the investigated compounds. For example, compounds 6d and 6e displayed MIC values of 9.40 and 9.00 µM, respectively, regarding S. aureus, and 4.70 and 4.50 µM, respectively, regarding S. pneumonia in comparison to ciprofloxacin (12.07 µM). The cytotoxicity of compounds 6d and 6e were performed on normal human WI-38 cell lines with IC50 values of 288.69 and 227.64 μM, respectively assuring their safety and selectivity. Besides, DNA gyrase inhibition assay of compounds 6d and 6e was carried out in comparison to ciprofloxacin, and interestingly, compounds 6d and 6e disclosed promising IC50 values of 0.242 and 0.177 μM, respectively, whereas ciprofloxacin displayed an IC50 value of 0.768 μM, assuring the proposed mechanism of action for the afforded compounds. Consequently, compounds 6d and 6e were further assessed via in-vivo approaches by evaluating blood counts, liver and kidney functions, and histopathological examination. Both compounds were found to be safer on the liver and kidney than the reference ciprofloxacin. Moreover, in-silico molecular docking studies were established and revealed reasonable binding affinities for all afforded compounds, particularly compound 6d which exhibited a binding score of -7.51 kcal/mol, surpassing the reference ciprofloxacin (-7.29 kcal/mol) with better anticipated stability at the DNA gyrase binding pocket. Moreover, ADME studies were conducted, disclosing an eligible bioavailability score of >0.55 for all afforded compounds, and reasonable GIT absorption without passing the blood brain barrier was attained for most investigated compounds, ensuring their efficacy and safety. Lastly, a structure activity relationship study for the synthesized compounds was established and unveiled that not only the main pharmacophores required for DNA gyrase inhibition are enough for exerting promising antimicrobial activities, but also derivatization with diverse aryl/hetero aryl aldehydes is essential for their enhanced antimicrobial potential.

Synthesis, Biological Evaluation and Machine Learning Prediction Model for Fluorinated Cinchona Alkaloid-Based Derivatives as Cholinesterase Inhibitors

A series of 46 Cinchona alkaloid derivatives that differ in positions of fluorine atom(s) in the molecule were synthesized and tested as human acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibitors. All tested compounds reversibly inhibited AChE and BChE in the nanomolar to micromolar range; for AChE, the determined enzyme-inhibitor dissociation constants (K_i) ranged from 3.9-80 µM, and 0.075-19 µM for BChE. The most potent AChE inhibitor was N-(para-fluorobenzyl)cinchoninium bromide, while N-(meta-fluorobenzyl)cinchonidinium bromide was the most potent BChE inhibitor with K_i constant in the nanomolar range. Generally, compounds were non-selective or BChE selective cholinesterase inhibitors, where N-(meta-fluorobenzyl)cinchonidinium bromide was the most selective showing 533 times higher preference for BChE. In silico study revealed that twenty-six compounds should be able to cross the blood-brain barrier by passive transport. An extensive machine learning procedure was utilized for the creation of multivariate linear regression models of AChE and BChE inhibition. The best possible models with predicted R² (CD-derivatives) of 0.9932 and R²(CN-derivatives) of 0.9879 were calculated and cross-validated. From these data, a smart guided search for new potential leads can be performed. These results pointed out that quaternary Cinchona alkaloids are the promising structural base for further development as selective BChE inhibitors which can be used in the central nervous system.

3D-QSAR, ADME-Tox In Silico Prediction and Molecular Docking Studies for Modeling the Analgesic Activity against Neuropathic Pain of Novel NR2B-Selective NMDA Receptor Antagonists

A new class of selective antagonists of the N-Methyl-D-Aspartate (NMDA) receptor subunit 2B have been developed using molecular modeling techniques. The three-dimensional quantitative structure–activity relationship (3D-QSAR) study, based on comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) models, indicate that steric, electrostatic and hydrogen bond acceptor fields have a key function in the analgesic activity against neuropathic pain. The predictive accuracy of the developed CoMFA model (Q2 = 0.540, R2 = 0.980, R2 pred = 0.613) and the best CoMSIA model (Q2 = 0.665, R2 = 0.916, R2 pred = 0.701) has been successfully examined through external and internal validation. Based on ADMET in silico properties, L1, L2 and L3 ligands are non-toxic inhibitors of 1A2, 2C19 and 2C9 cytochromes, predicted to passively cross the blood–brain barrier (BBB) and have the highest probability to penetrate the central nervous system (CNS). Molecular docking results indicate that the active ligands (L1, L2 and L3) interact specifically with Phe176, Glu235, Glu236, Gln110, Asp136 and Glu178 amino acids of the transport protein encoded as 3QEL. Therefore, they could be used as analgesic drugs for the treatment of neuropathic pain.

Synthesis of novel carboxamide- and carbohydrazide-benzimidazoles as selective butyrylcholinesterase inhibitors

Selectively inhibiting butyrylcholinesterase (BChE) is hypothesized to help in the management of Alzheimer's disease (AD). Several studies have determined a correlation between the increased activity of BChE and the onset of AD. An advantage of BChE over acetylcholinesterase inhibition is that absence of BChE activity does not lead to obvious physiological disturbance. However, currently no BChE inhibitors are available commercially as potential therapeutics for AD. In our continuous effort to find potent BChE inhibitors for Alzheimer's disease, a total of 22 novel benzimidazoles with diversified substitutions were synthesized and evaluated for their anticholinesterase activities in this study. Among the synthesized compounds, 2j and 3f were found to exhibit potent and selective BChE inhibition with IC₅₀ values of 1.13 and 1.46 μM, respectively. Molecular docking studies were carried out to rationalize the observed inhibitory activities. The compounds were predicted to have high penetration across the blood-brain barrier. Moreover, cell proliferative studies were also performed to evaluate the toxicity profile of the interested compounds. Compound 3f was found to be a potent and selective butyrylcholinesterase inhibitor with an IC₅₀ value of 1.46 µM.

Target-based virtual screening, computational multiscoring docking and molecular dynamics simulation of small molecules as promising drug candidate affecting kinesin-like protein KIFC1

The kinesin family member C1 (KIFC1) is an essential protein that facilitates the bipolar division of neoplastic cells. Inhibiting KIFC1 by small molecules is a lucrative strategy to impede bipolar mitosis leading to the apoptosis of cancerous cells. The research aims to envisage small-molecule inhibitors targeting KIFC1. The Mcule database, a comprehensive online digital platform containing more than five million chemical compounds, was used for structure-based virtual screening (SBVS). Druglikeness filtration sifted 2,293,282 chemical hits that further narrowed down to 49 molecules after toxicity profiling. Finally, 39 compounds that comply with the BOILED-Egg permeation predictive model of the ADME rules were carried forward for multiscoring docking using the AutoDock Vina inbuilt to Mcule drug discovery platform, DockThor and SwissDock tools. The mean of ΔG terms produced by docking tools was computed to find consensus top ligand hits. AZ82 exhibited stronger binding (Consensus ΔG: -7.99 kcal mol^-1 ) with KIFC1 among reference inhibitors, for example, CW069 (-7.57 kcal mol^-1 ) and SR31527 (-7.01 kcal mol^-1 ). Ten ligand hits namely, Mcule-4895338547 (Consensus ΔG: -8.69 kcal mol^-1 ), Mcule-7035674888 (-8.42 kcal mol^-1 ), Mcule-5531166845 (-8.53 kcal mol^-1 ), Mcule-3248415882 (-8.55 kcal mol^-1 ), Mcule-291881733 (-8.41 kcal mol^-1 ), Mcule-5918624394 (-8.44), Mcule-3470115427 (-8.47), Mcule-3686193135 (-8.18 kcal mol^-1 ), Mcule-3955355291 (8.09 kcal mol^-1 ) and Mcule-9534899193 (-8.01 kcal mol^-1 ) depicted strong binding interactions with KIFC1 in comparison to potential reference inhibitor AZ82. The top four ligands and AZ82 were considered for molecular dynamics simulation of 50 ns duration. Toxicity profiling, physicochemical properties, lipophilicity, solubility, pharmacokinetics, druglikeness, medicinal chemistry attributes, average potential energy, RMSD, RMSF, SASA, ΔGsolv and Rg analyses forecast the ligand mcule-4895338547 as a promising inhibitor of KIFC1.

Integration of Ligand-Based and Structure-Based Methods for the Design of Small-Molecule TLR7 Antagonists

Toll-like receptor 7 (TLR7) is activated in response to the binding of single-stranded RNA. Its over-activation has been implicated in several autoimmune disorders, and thus, it is an established therapeutic target in such circumstances. TLR7 small-molecule antagonists are not yet available for therapeutic use. We conducted a ligand-based drug design of new TLR7 antagonists through a concerted effort encompassing 2D-QSAR, 3D-QSAR, and pharmacophore modelling of 54 reported TLR7 antagonists. The developed 2D-QSAR model depicted an excellent correlation coefficient (R²_training: 0.86 and R²_test: 0.78) between the experimental and estimated activities. The ligand-based drug design approach utilizing the 3D-QSAR model (R²_training: 0.95 and R²_test: 0.84) demonstrated a significant contribution of electrostatic potential and steric fields towards the TLR7 antagonism. This consolidated approach, along with a pharmacophore model with high correlation (R_training: 0.94 and R_test: 0.92), was used to design quinazoline-core-based hTLR7 antagonists. Subsequently, the newly designed molecules were subjected to molecular docking onto the previously proposed binding model and a molecular dynamics study for a better understanding of their binding pattern. The toxicity profiles and drug-likeness characteristics of the designed compounds were evaluated with in silico ADMET predictions. This ligand-based study contributes towards a better understanding of lead optimization and the future development of potent TLR7 antagonists.

4-Aminoquinoline-Based Adamantanes as Potential Anticholinesterase Agents in Symptomatic Treatment of Alzheimer's Disease

Considering that acetylcholinesterase (AChE) inhibition is the most important mode of action expected of a potential drug used for the treatment of symptoms of Alzheimer's disease (AD), our previous pilot study of 4-aminoquinolines as potential human cholinesterase inhibitors was extended to twenty-two new structurally distinct 4-aminoquinolines bearing an adamantane moiety. Inhibition studies revealed that all of the compounds were very potent inhibitors of AChE and butyrylcholinesterase (BChE), with inhibition constants (Ki) ranging between 0.075 and 25 µM. The tested compounds exhibited a modest selectivity between the two cholinesterases; the most selective for BChE was compound 14, which displayed a 10 times higher preference, while compound 19 was a 5.8 times more potent inhibitor of AChE. Most of the compounds were estimated to be able to cross the blood-brain barrier (BBB) by passive transport. Evaluation of druglikeness singled out fourteen compounds with possible oral route of administration. The tested compounds displayed modest but generally higher antioxidant activity than the structurally similar AD drug tacrine. Compound 19 showed the highest reducing power, comparable to those of standard antioxidants. Considering their simple structure, high inhibition of AChE and BChE, and ability to cross the BBB, 4-aminoquinoline-based adamantanes show promise as structural scaffolds for further design of novel central nervous system drugs. Among them, two compounds stand out: compound 5 as the most potent inhibitor of both cholinesterases with a Ki constant in low nano molar range and the potential to cross the BBB, and compound 8, which met all our requirements, including high cholinesterase inhibition, good oral bioavailability, and antioxidative effect. The QSAR model revealed that AChE and BChE inhibition was mainly influenced by the ring and topological descriptors MCD, Nnum, RP, and RSIpw3, which defined the shape, conformational flexibility, and surface properties of the molecules.

In silico study of potential antiviral activity of copper(II) complexes with non-steroidal anti-inflammatory drugs on various SARS-CoV-2 target proteins

In silico molecular docking studies, in vitro toxicity and in silico predictions on the biological activity profile, pharmacokinetic properties, drug-likeness, ADMET (absorption, distribution, metabolism, excretion, and toxicity) physicochemical pharmacokinetic data, and target proteins and toxicity predictions were performed on six copper(II) complexes with the non-steroidal anti-inflammatory drugs ibuprofen, loxoprofen, fenoprofen and clonixin as ligands, in order to investigate the ability of these complexes to interact with the key therapeutic target proteins of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) 3C-like cysteine main protease (3CLpro/Mpro), viral papain-like protease (PLpro), RNA-dependent RNA polymerase (RdRp), and non-structural proteins (Nsps) Nsp16-Nsp10 2'-O-methyltransferase complex, and their capacity to act as antiviral agents, contributing thus to understanding the role they can play in the context of coronavirus 2019 (COVID-19) pandemic. Cytotoxic activity against five human cancer and normal cell lines were also evaluated.

QSAR, ADMET In Silico Pharmacokinetics, Molecular Docking and Molecular Dynamics Studies of Novel Bicyclo (Aryl Methyl) Benzamides as Potent GlyT1 Inhibitors for the Treatment of Schizophrenia

Forty-four bicyclo ((aryl) methyl) benzamides, acting as glycine transporter type 1 (GlyT1) inhibitors, are developed using molecular modeling techniques. QSAR models generated by multiple linear and non-linear regressions affirm that the biological inhibitory activity against the schizophrenia disease is strongly and significantly correlated with physicochemical, geometrical and topological descriptors, in particular: Hydrogen bond donor, polarizability, surface tension, stretch and torsion energies and topological diameter. According to in silico ADMET properties, the most active ligands (L6, L9, L30, L31 and L37) are the molecules having the highest probability of penetrating the central nervous system (CNS), but the molecule 32 has the highest probability of being absorbed by the gastrointestinal tract. Molecular docking results indicate that Tyr124, Phe43, Phe325, Asp46, Phe319 and Val120 amino acids are the active sites of the dopamine transporter (DAT) membrane protein, in which the most active ligands can inhibit the glycine transporter type 1 (GlyT1). The results of molecular dynamics (MD) simulation revealed that all five inhibitors remained stable in the active sites of the DAT protein during 100 ns, demonstrating their promising role as candidate drugs for the treatment of schizophrenia.

Bioprospecting of an Endolichenic Fungus Phanerochaete sordida Isolated from Mangrove-Associated Lichen Bactrospora myriadea

Bioassay-guided fractionation of the ethyl acetate extract of Phanerochaete sordida, an endolichenic fungus (ELF) isolated from the host lichen Bactrospora myriadea, collected from Negombo lagoon, Sri Lanka, led to the isolation of a bioactive compound. Following the identification of the fungus using morphological and DNA barcoding techniques, the pure compound was isolated using column chromatography, preparative TLC, and semipreparative HPLC. The structure elucidation was carried out using IR, HR-ESI-MS and 1H, 13C & 2D NMR spectroscopic methods. The in vitro bioassays conducted revealed that compound 1 has a high antioxidant activity with ABTS•+ (IC50 $58.91\pm 1.35\mu \text{M}$ ), moderate anti-inflammatory activity (IC50 $254.79\pm 1.41\mu \text{M}$ ), comparable antibacterial activity against the oral-bacterial strain Streptococcus mutans (MIC 898.79 μM and MLC 1797.58 μM), moderate tyrosinase inhibition (IC50 $1713.69\pm 8.65\mu \text{M}$ ), and moderate cytotoxicity against oral cancer (IC50 $13.65\pm 0.02\mu \text{M}$ ), in comparison with respective positive controls. The in silico experiments conducted for tyrosinase inhibition and cytotoxicity using Schrödinger revealed results in line with the in vitro results, thus confirming the bioactivities. The molecule also satisfies the key features of drug likeliness according to pharmacokinetic studies.

Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning

Coronaviruses, including the recent pandemic strain SARS-Cov-2, use a multifunctional 2'-O-methyltransferase (2'-O-MTase) to restrict the host defense mechanism and to methylate RNA. The nonstructural protein 16 2'-O-MTase (nsp16) becomes active when nonstructural protein 10 (nsp10) and nsp16 interact. Novel peptide drugs have shown promise in the treatment of numerous diseases and new research has established that nsp10 derived peptides can disrupt viral methyltransferase activity via interaction of nsp16. This study had the goal of optimizing new analogous nsp10 peptides that have the ability to bind nsp16 with equal to or higher affinity than those naturally occurring. The following research demonstrates that in silico molecular simulations can shed light on peptide structures and predict the potential of new peptides to interrupt methyltransferase activity via the nsp10/nsp16 interface. The simulations suggest that misalignments at residues F68, H80, I81, D94, and Y96 or rotation at H80 abrogate MTase function. We develop a new set of peptides based on conserved regions of the nsp10 protein in the Coronaviridae species and test these to known MTase variant values. This results in the prediction that the H80R variant is a solid new candidate for potential new testing. We envision that this new lead is the beginning of a reputable foundation of a new computational method that combats coronaviruses and that is beneficial for new peptide drug development.

A Series of Furimazine Derivatives for Sustained Live-Cell Bioluminescence Imaging and Application to the Monitoring of Myogenesis at the Single-Cell Level

Bioluminescence (BL) imaging, which utilizes light emitted through the enzymatic reaction of luciferase oxidizing its substrate luciferin, enables sensitive and noninvasive monitoring of life phenomena. Herein, we developed a series of caged furimazine (FMZ) derivatives by introducing a protective group at the C-3 position and a hydroxy group at the C-6 phenyl ring to realize long-term live-cell BL imaging based on the NanoLuc (NLuc)/NanoKAZ (NKAZ)-FMZ system. The membrane permeability and cytotoxicity of the substrates were evaluated and related to their hydrophobicity. Among the series, the derivative with the bulkiest protective group (adamantanecarbonyl group) and a hydroxy substituent (named Ad-FMZ-OH) showed significantly prolonged and constant BL signal in cells expressing NLuc compared to the native FMZ substrate. This derivative enabled continuous BL imaging at the single-cell level for 24 h. Furthermore, we applied Ad-FMZ-OH to BL imaging of myocyte fusion and succeeded in the consecutive and sensitive monitoring at a single-cell level over a day. In summary, NLuc/NKAZ-caged FMZ derivatives have the potential to be applied to live-cell BL imaging of various life phenomena that require long-term observation.