Identification of Potential COX-2 Inhibitors for the Treatment of Inflammatory Diseases Using Molecular Modeling Approaches

Leveraging shape screening and molecular dynamics simulations to optimize PARP1-Specific chemo/radio-potentiators for antitumor drug design

PARP1 plays a pivotal role in DNA repair within the base excision pathway, making it a promising therapeutic target for cancers involving BRCA mutations. Current study is focused on the discovery of PARP inhibitors with enhanced selectivity for PARP1. Concurrent inhibition of PARP1 with PARP2 and PARP3 affects cellular functions, potentially causing DNA damage accumulation and disrupting immune responses. In step 1, a virtual library of 593 million compounds has been screened using a shape-based screening approach to narrow down the promising scaffolds. In step 2, hierarchical docking approach embedded in Schrödinger suite was employed to select compounds with good dock score, drug-likeness and MMGBSA score. Analysis supplemented with decomposition energy, molecular dynamics (MD) simulations and hydrogen bond frequency analysis, pinpointed that active site residues; H862, G863, R878, M890, Y896 and F897 are crucial for specific binding of ZINC001258189808 and ZINC000092332196 with PARP1 as compared to PARP2 and PARP3. The binding of ZINC000656130962, ZINC000762230673, ZINC001332491123, and ZINC000579446675 also revealed interaction involving two additional active site residues of PARP1, namely N767 and E988. Weaker or no interaction was observed for these residues with PARP2 and PARP3. This approach advances our understanding of PARP-1 specific inhibitors and their mechanisms of action, facilitating the development of targeted therapeutics.

Role of multi-targeted bioactive natural molecules and their derivatives in the treatment of Alzheimer's disease: an insight into structure-activity relationship

Alzheimer's disease (AD) is a complex neurodegenerative disorder involving cognitive dysfunction like short-term memory and behavioral changes as the disease progresses due to other unaltered physiological factors. The solution for this problem is Multi-targeted Drugs (MTDs), which can affect multiple determinants to realize the multifunctional effects. Acetylcholinesterase (AChE) inhibitors donepezil, rivastigmine, galantamine, and N-methyl-D-aspartate (NMDA) receptor antagonist memantine are FDA-approved drugs used to treat AD symptomatically. The key objective of this review is to understand multitargeted bioactive natural molecules that could be considered as leads for further development as effective drugs for treating AD, along with understanding its pharmacology and structure-activity relationship (SAR). Understanding the molecular mechanism of the AD pathophysiology, the role of existing drugs, treatment of AD via amyloid beta (Aβ) plaque, and neurofibrillary tangle (NFT) inhibition by natural bioactive molecules were also discussed in the review. The current quest and recent advancements with natural bioactive compounds like physostigmine, resveratrol, curcumin, and catechins, along with the study of in silico SAR, were reported in the present study. This review summarises the structural properties required for bioactive natural molecules to show anti-Alzheimer's activity by emphasizing on SAR of several bioactive natural molecules targeting various AD pathologies, their key molecular interactions that are critical for target specificity, their role as multitargeted ligands, used with adjunctive therapy for AD followed by related US patents granted recently. This article highlights the significance of the structural features of natural bioactive molecules in the treatment of AD and establishes a connection between them.Communicated by Ramaswamy H. Sarma.

Synthesis, anti-inflammatory activity, and conformational relationship studies of chromone derivatives incorporating amide groups

Inflammation is the initial biological reaction of the immune system to various stimuli such as infection, injury, or irritation. Extensive research has demonstrated that a growing array of diseases are triggered by inflammatory mechanisms. Currently, anti-inflammatory drugs are widely utilized in clinical practice due to their therapeutic advantages; however, the potential side effects cannot be ignored by us. In our work, a series of amide compounds with chromones as the parent nucleus were designed and synthesized using the principle of colligated drug design. The results of the biological evaluation indicated that four compounds exhibited lower EC50 values compared to the positive drug ibuprofen. Notably, compound 5-9 showed optimal inhibitory activity (EC50 = 5.33 ± 0.57 μM) against the production of nitric oxide (NO) induced by lipopolysaccharide (LPS) in RAW264.7 cells. Structure-activity relationships (SAR) showed that the presence of electron-withdrawing groups at positions 5 and 8, or electron-donating groups at positions 6 and 7 of the parent nucleus of the chromones can enhance the anti-inflammatory activity of the chromones. The molecular docking studies predicted the mode of interaction between the compounds and protein. Additionally, these studies have demonstrated that the amide bond is the key radical to the anti-inflammatory effect. Based on the summary of the aforementioned studies, it can be inferred that compound 5-9 exhibit potential as an anti-inflammatory drug that deserves further investigation.

Analgesic Activity of 5-Acetamido-2-Hydroxy Benzoic Acid Derivatives and an In-Vivo and In-Silico Analysis of Their Target Interactions

The design, synthesis, and evaluation of novel non-steroidal anti-inflammatory drugs (NSAIDs) with better activity and lower side effects are big challenges today. In this work, two 5-acetamido-2-hydroxy benzoic acid derivatives were proposed, increasing the alkyl position (methyl) in an acetamide moiety, and synthesized, and their structural elucidation was performed using 1H NMR and 13C NMR. The changes in methyl in larger groups such as phenyl and benzyl aim to increase their selectivity over cyclooxygenase 2 (COX-2). These 5-acetamido-2-hydroxy benzoic acid derivatives were prepared using classic methods of acylation reactions with anhydride or acyl chloride. Pharmacokinetics and toxicological properties were predicted using computational tools, and their binding affinity (kcal/mol) with COX-2 receptors (Mus musculus and Homo sapiens) was analyzed using docking studies (PDB ID 4PH9, 5KIR, 1PXX and 5F1A). An in-silico study showed that 5-acetamido-2-hydroxy benzoic acid derivates have a better bioavailability and binding affinity with the COX-2 receptor, and in-vivo anti-nociceptive activity was investigated by means of a writhing test induced by acetic acid and a hot plate. PS3, at doses of 20 and 50 mg/kg, reduced painful activity by 74% and 75%, respectively, when compared to the control group (20 mg/kg). Regarding the anti-nociceptive activity, the benzyl showed reductions in painful activity when compared to acetaminophen and 5-acetamido-2-hydroxy benzoic acid. However, the proposed derivatives are potentially more active than 5-acetamido-2-hydroxy benzoic acid and they support the design of novel and safer derivative candidates. Consequently, more studies need to be conducted to evaluate the different pharmacological actions, the toxicity of possible metabolites that can be generated, and their potential use in inflammation and pain therapy.

In-vitro and computational analysis of Urolithin-A for anti-inflammatory activity on Cyclooxygenase 2 (COX-2)

Cyclooxygenase 2 (COX-2) participates in the inflammation process by converting arachidonic acid into prostaglandin G2 which increases inflammation, pain and fever. COX-2 has an active site and a heme pocket and blocking these sites stops the inflammation. Urolithin A is metabolite of ellagitannin produced from humans and animals gut microbes. In the current study, Urolithin A showed good pharmacokinetic properties. Molecular docking of the complex of Urolithin A and COX-2 revealed the ligand affinity of -7.97 kcal/mol with the ligand binding sites at TYR355, PHE518, ILE517 and GLN192 with the 4-H bonds at a distance of 2.8 Å, 2.3 Å, 2.5 Å and 1.9 Å. The RMSD plot for Urolithin A and COX-2 complex was observed to be constant throughout the duration of dynamics. A total of 3 pair of hydrogen bonds was largely observed on average of 3 simulation positions for dynamics duration of 500 ns. The MMPBSA analysis showed that active site amino acids had a binding energy of -22.0368 kJ/mol indicating that throughout the simulation the protein of target was bounded by Urolithin A. In-silico results were validated by biological assays. Urolithin A strongly revealed to exhibit anti-inflammatory effect on COX-2 with an IC50 value of 44.04 µg/mL. The anti-inflammatory capability was also depicted through reduction of protein denaturation that showed 37.6 ± 0.1 % and 43.2 ± 0.07 % reduction of protein denaturation for BSA and egg albumin respectively at 500 µg/mL. The present study, suggests Urolithin A to be an effective anti-inflammatory compound for therapeutic use.

Alkaloid from Geissospermum sericeum Benth. & Hook.f. ex Miers (Apocynaceae) Induce Apoptosis by Caspase Pathway in Human Gastric Cancer Cells

Gastric cancer is among the major causes of death from neoplasia leading causes of death worldwide, with high incidence rates and problems related to its treatment. Here, we outline how Geissospermum sericeum exerts antitumor activity on the ACP02 cell line (human gastric adenocarcinoma) and the mechanism of cell death. The ethanol extract and fractions, neutral fraction and alkaloid fraction, were characterized by thin-layer chromatography and HPLC-DAD, yielding an alkaloid (geissoschizoline N4-methylchlorine) identified by NMR. The cytotoxicity activity of the samples (ethanol extract, neutral fraction, alkaloid fraction, and geissoschizoline N4-methylchlorine) in HepG2 and VERO cells was determined by MTT. The ACP02 cell line was used to assess the anticancer potential. Cell death was quantified with the fluorescent dyes Hoechst 33342, propidium iodide, and fluorescein diacetate. The geissoschizoline N4-methylchlorine was evaluated in silico against caspase 3 and 8. In the antitumor evaluation, there was observed a more significant inhibitory effect of the alkaloid fraction (IC50 18.29 µg/mL) and the geissoschizoline N4-methylchlorine (IC₅₀ 12.06 µg/mL). However, geissoschizoline N4-methylchlorine showed lower cytotoxicity in the VERO (CC₅₀ 476.0 µg/mL) and HepG2 (CC₅₀ 503.5 µg/mL) cell lines, with high selectivity against ACP02 cells (SI 39.47 and 41.75, respectively). The alkaloid fraction showed more significant apoptosis and necrosis in 24 h and 48 h, with increased necrosis in higher concentrations and increased exposure time. For the alkaloid, apoptosis and necrosis were concentration- and time-dependent, with a lower necrosis rate. Molecular modeling studies demonstrated that geissoschizoline N4-methylchlorine could occupy the active site of caspases 3 and 8 energetically favorably. The results showed that fractionation contributed to the activity with pronounced selectivity for ACP02 cells, and geissoschizoline N4-methylchlor is a promising candidate for caspase inhibitors of apoptosis in gastric cancer. Thus, this study provides a scientific basis for the biological functions of Geissospermum sericeum, as well as demonstrates the potential of the geissoschizoline N4-methylchlorine in the treatment of gastric cancer.

Design and Identification of Inhibitors for the Spike-ACE2 Target of SARS-CoV-2

When an epidemic started in the Chinese city of Wuhan in December 2019, coronavirus was identified as the cause. Infection by the virus occurs through the interaction of viral S protein with the hosts' angiotensin-converting enzyme 2. By leveraging resources such as the DrugBank database and bioinformatics techniques, ligands with potential activity against the SARS-CoV-2 spike protein were designed and identified in this investigation. The FTMap server and the Molegro software were used to determine the active site of the Spike-ACE2 protein's crystal structure. Virtual screening was performed using a pharmacophore model obtained from antiparasitic drugs, obtaining 2000 molecules from molport^®. The ADME/Tox profiles were used to identify the most promising compounds with desirable drug characteristics. The binding affinity investigation was then conducted with selected candidates. A molecular docking study showed five structures with better binding affinity than hydroxychloroquine. Ligand_003 showed a binding affinity of -8.645 kcal·mol^-1, which was considered an optimal value for the study. The values presented by ligand_033, ligand_013, ligand_044, and ligand_080 meet the profile of novel drugs. To choose compounds with favorable potential for synthesis, synthetic accessibility studies and similarity analyses were carried out. Molecular dynamics and theoretical IC₅₀ values (ranging from 0.459 to 2.371 µM) demonstrate that these candidates are promising for further tests. Chemical descriptors showed that the candidates had strong molecule stability. Theoretical analyses here show that these molecules have potential as SARS-CoV-2 antivirals and therefore warrant further investigation.

Revealing the drug resistance mechanism of saquinavir due to G48V and V82F mutations in subtype CRF01_AE HIV-1 protease: molecular dynamics simulation and binding free energy calculations

Human immunodeficiency virus-1 (HIV-1) protease is one of the important targets in AIDS therapy. The majority of HIV infections are caused due to non-B subtypes in developing countries. The co-occurrence of mutations along with naturally occurring polymorphisms in HIV-1 protease cause resistance to the FDA approved drugs, thereby posing a major challenge in the treatment of antiretroviral therapy. In this work, the resistance mechanism against SQV due to active site mutations G48V and V82F in CRF01_AE (AE) protease was explored. The binding free energy calculations showed that the direct substitution of valine at position 48 introduces a bulkier side chain, directly impairing the interaction with SQV in the binding pocket. Also, the intramolecular hydrogen bonding network of the neighboring residues is altered, indirectly affecting the binding of SQV. Interestingly, the substitution of phenylalanine at position 82 induces conformational changes in the 80's loop and the flap region, thereby favoring the binding of SQV. The V82F mutant structure also maintains similar intramolecular hydrogen bond interactions as observed in AE-WT.Communicated by Ramaswamy H. Sarma.

Identification of human phosphoglycerate mutase 1 (PGAM1) inhibitors using hybrid virtual screening approaches

PGAM1 plays a critical role in cancer cell metabolism through glycolysis and different biosynthesis pathways to promote cancer. It is generally known as a crucial target for treating pancreatic ductal adenocarcinoma, the deadliest known malignancy worldwide. In recent years different studies have been reported that strived to find inhibitory agents to target PGAM1, however, no validated inhibitor has been reported so far, and only a small number of different inhibitors have been reported with limited potency at the molecular level. Our in silico studies aimed to identify potential new PGAM1 inhibitors that could bind at the allosteric sites. At first, shape and feature-based models were generated and optimized by performing receiver operating characteristic (ROC) based enrichment studies. The best query model was then employed for performing shape, color, and electrostatics complementarity-based virtual screening of the ChemDiv database. The top two hundred and thirteen hits with greater than 1.2 TanimotoCombo score were selected and then subjected to structure-based molecular docking studies. The hits yielded better docking scores than reported compounds, were selected for subsequent structural similarity-based clustering analysis to select the best hits from each cluster. Molecular dynamics simulations and binding free energy calculations were performed to validate their plausible binding modes and their binding affinities with the PGAM1 enzyme. The results showed that these compounds were binding in the reported allosteric site of the enzyme and can serve as a good starting point to design better active selective scaffolds against PGAM1enzyme.

Juvenile hormone mimics with phenyl ether and amide functionality to be insect growth regulators (IGRs): synthesis, characterization, computational and biological study

A series of substituted phenyl ethers derivatives as juvenile hormone (JH) mimics (V₁-V₈) have been synthesized. Substituted phenoxyacetic acid and amino acid ethyl ester hydrochloride were prepared using NaOH, SOCl₂. DCC method has been used for amide linkage. The structure of prepared compounds has been confirmed by Fourier Transform Infra-Red (FT-IR), Electrospray ionization-Mass spectrometry (ESI-MS), Proton and Carbon-13 nuclear magnetic resonance (¹H-NMR, ¹³C-NMR) spectroscopic techniques. Biological efficacy of synthesized analogs has been carried out under laboratory conditions. Galleria mellonella (honey bee pest) has been chosen as testing insect. Juvenile hormone (JH) activity of synthesized compounds has been tested at different concentrations and compared with the standard juvenile hormone analogs (JHAs) pyriproxyfen (M₁) and fenoxycarb (M₂) against the fifth larval instar of G. mellonella. Compound ethyl 2-[2-(4-methylphenoxy)aminoacetyl]-3-phenyl-propanoate (V₆) exhibited better activity among all the synthesized compounds (V₁-V₈) with LC₅₀ and LC₉₀ values of 0.11 mg/mL and 0.56 mg/mL respectively. Compounds showed insect growth regulating (IGR) activity at lower concentrations. In silico screening of all synthesized compounds with the W-cavity of juvenile hormone-binding protein (JHBP) of insect G. mellonella has been carried out. Chemical reactivity of synthesized series has been studied using DFT/B3LYP/6-311 + G(d,2p) method. Non-toxic behavior of molecules has also been observed from ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) study using discovery studio client 3.0.Communicated by Ramaswamy H. Sarma.

Acute Toxicity and Anti-Inflammatory Activity of Trattinnickia rhoifolia Willd (Sucuruba) Using the Zebrafish Model

The species Trattinnickia rhoifolia Willd, (T. rhoifolia), which belongs to the Burseraceae family, is widely used in ethnopharmacological cultural practices by traditional Amazonian people for anti-inflammatory purposes, sometimes as their only therapeutic resource. Although it is used in teas, infusions, macerations and in food, the species is still unexplored in regard to its pharmacophoric potential and chemical profile. Therefore, the aim of this study was to conduct a phytochemical characterization of the hydroethanolic extract of T. rhoifolia leaves (HELTr) and to evaluate the acute toxicity and anti-inflammatory activity of this species using zebrafish (Danio rerio). The extract was analyzed by gas chromatography−mass spectrometry (GC-MS). The evaluation of the acute toxicity of the HELTr in adult zebrafish was determined using the limit test (2000 mg/kg), with behavioral and histopathological evaluations, in addition to the analysis of the anti-inflammatory potential of HELTr in carrageenan-induced abdominal edema, followed by the use of the computational method of molecular docking. The phytochemical profile of the species is chemically diverse, suggesting the presence of the fatty acids, ester, alcohol and benzoic acid classes, including propanoic acid, ethyl ester and hexadecanoic acid. In the studies of zebrafish performed according to the index of histopathological changes (IHC), the HELTr did not demonstrate toxicity in the behavioral and histopathological assessments, since the vital organs remained unchanged. Carrageenan-induced abdominal edema was significantly reduced at all HELTr doses (100, 200 and 500 mg/kg) in relation to the negative control, dimethyl sulfoxide (DMSO), while the 200 mg/kg dose showed significant anti-inflammatory activity in relation to the positive control (indomethacin). With these activities being confirmed by molecular docking studies, they showed a good profile for the inhibition of the enzyme Cyclooxygenase-2 (COX-2), as the interactions established at the sites of the receptors used in the docking study were similar to the controls (RCX, IMN and CEL). Therefore, the HELTr has an acceptable degree of safety for acute toxicity, defined in the analysis of behavioral changes, mortality and histopathology, with a significant anti-inflammatory action in zebrafish at all doses, which demonstrates the high pharmacophoric potential of the species. These results may direct future applications and drug development but still require further elucidation.

In Silico Evaluation of the Antimicrobial Activity of Thymol-Major Compounds in the Essential Oil of Lippia thymoides Mart. & Schauer (Verbenaceae)

In this paper, we evaluated the drug-receptor interactions responsible for the antimicrobial activity of thymol, the major compound present in the essential oil (EO) of Lippia thymoides (L. thymoides) Mart. & Schauer (Verbenaceae). It was previously reported that this EO exhibits antimicrobial activity against Candida albicans (C. albicans), Staphylococcus aureus (S. aureus), and Escherichia coli (E. coli). Therefore, we used molecular docking, molecular dynamics simulations, and free energy calculations to investigate the interaction of thymol with pharmacological receptors of interest to combat these pathogens. We found that thymol interacted favorably with the active sites of the microorganisms’ molecular targets. MolDock Score results for systems formed with CYP51 (C. albicans), Dihydrofolate reductase (S. aureus), and Dihydropteroate synthase (E. coli) were −77.85, −67.53, and −60.88, respectively. Throughout the duration of the MD simulations, thymol continued interacting with the binding pocket of the molecular target of each microorganism. The van der Waals (ΔE_vdW = −24.88, −26.44, −21.71 kcal/mol, respectively) and electrostatic interaction energies (ΔE_ele = −3.94, −11.07, −12.43 kcal/mol, respectively) and the nonpolar solvation energies (ΔG_NP = −3.37, −3.25, −2.93 kcal/mol, respectively) were mainly responsible for the formation of complexes with CYP51 (C. albicans), Dihydrofolate reductase (S. aureus), and Dihydropteroate synthase (E. coli).

Investigation on anti-Corona viral potential of Yarrow tea

Achillea millefolium (Yarrow) is a herbaceous plant of Greek origin noted to treat pneumonia, common cold, cough, and other respiratory disorders. The flowers and leaves are the core part used to prepare herbal tea that gains the world's recognition as medicinal tea. Coronavirus disease is spreading across the globe, and numerous approaches are lodged to treat virus-induced lung inflammation. Here, we used the network pharmacology, metabolite analysis, docking and molecular simulation and MM-PBSA analysis to comprehend the biochemical basis of the health-boosting impact of Yarrow tea. Next, we performed the microscopic and dynamic light scattering (DLS) analysis of yarrow-treated ChAdOx1 nCoV-19 to evaluate the virucidal activity of the Yarrow. The present study investigates the druggability, metabolites and potential interaction of the title tea with genes associated with Covid-19-induced pathogenesis. Towards this, 1022 gene hits were obtained, 30 are mutually shared. Network Pharmacology and microarray gene expression analysis find the connection of PTGS2 in relieving the virus-induced inflammation. Yarrow constituents Luteolin may inhibit or down-regulate the Cyclooxygenase II (PTGS2), a plausible mechanism underlying the Yarrow's anti-inflammatory actions. Further, the Yarrow's virucidal activity was assessed towards Transmission Electron Microscopic (TEM). The Yarrow treated SARS-nCoV-2 cell exhibits the disintegration of the virus membrane. This work provides a scientific basis for further elucidating the mechanism underlying Achillea millefolium's antiviral and anti-inflammatory properties.

Non-steroidal anti-inflammatory drugs: recent advances in the use of synthetic COX-2 inhibitors

Cyclooxygenase (COX) enzymes comprise COX-1 and COX-2 isoforms and are responsible for prostaglandin production. Prostaglandins have critical roles in the inflammation pathway and must be controlled by administration of selective nonsteroidal anti-inflammatory drugs (NSAIDs). Selective COX-2 inhibitors have been among the most used NSAIDs during the ongoing coronavirus 2019 pandemic because they reduce pain and protect against inflammation-related diseases. In this framework, the mechanism of action of both COX isoforms (particularly COX-2) as inflammation mediators must be reviewed. Moreover, proinflammatory cytokines such as tumor necrosis factor-α and interleukin (IL)-6, IL-1β, and IL-8 must be highlighted due to their major participation in upregulation of the inflammatory reaction. Structural and functional analyses of selective COX-2 inhibitors within the active-site cavity of COXs could enable introduction of lead structures with higher selectivity and potency against inflammation with fewer adverse effects. This review focuses on the biological activity of recently discovered synthetic COX-2, dual COX-2/lipoxygenase, and COX-2/soluble epoxide hydrolase hybrid inhibitors based primarily on the active motifs of related US Food and Drug Administration-approved drugs. These new agents could provide several advantages with regard to anti-inflammatory activity, gastrointestinal protection, and a safer profile compared with those of the NSAIDs celecoxib, valdecoxib, and rofecoxib.

Identification of dual binding mode of Orthodiffenes towards human topoisomerase-I and α-tubulin: exploring the potential role in anti-cancer activity via in silico study

The drugs prescribed for targeting the tumour growth comprise of chemotherapy regimen involving combinations to cell-cycle phase specific target receptors. The combination therapy with Topoisomerase-I (Topo-I) & anti-tubulin agents are in the clinical trial stages and have scope for identifying new chemical entities with dual binding and inhibiting potential. The checkpoint proteins present at the interface of cell-cycle phases are considered the link between these two that establish the connectivity across the two phases of cell-cycle. In the present study, this potential cross-link or dual targeting is explored via in silico analysis on the natural molecules, Orthodiffene (OD) A-F which are reported from the medicinal plant, Orthosiphon diffusus. These molecules have been reported to possess significant cytotoxicity against Jurkat and HL-60 cancer cells lines in vitro. A detailed in silico analysis on OD-series molecules to evaluate their plausible anticancer mechanism & potential, as well as their in situ ADMET profile study is reported here. The DFT analysis, molecular modelling and molecular dynamics (MD) collectively establishes Topoisomerase-I & α-Tubulin proteins to be the putative target responsible for the cytotoxic activities of OD-B. Orthodiffene series molecules found to be abiding by Lipinksi's rule of 5 for orally bioavailable drug molecule. The present data & study are useful for further exploration of developing new chemical entities based on the structures of OD-series molecules as dual-target inhibitors of Topo-I & tubulin proteins with better efficacies.

Molecular dynamics and structure-based virtual screening and identification of natural compounds as Wnt signaling modulators: possible therapeutics for Alzheimer's disease

Wnt signaling pathway is an evolutionarily conserved pathway responsible for neurogenesis, axon outgrowth, neuronal polarity, synapse formation, and maintenance. Downregulation of Wnt signaling has been found in patients with Alzheimer’s disease (AD). Several experimental approaches to activate Wnt signaling pathway have proven to be beneficial in alleviating AD, which is one of the new therapeutic approaches for AD. The current study focuses on the computational structure-based virtual screening followed by the identification of potential phytomolecules targeting different markers of Wnt signaling like WIF1, DKK1, LRP6, GSK-3β, and acetylcholine esterase. Initially, screening of 1924 compounds from the plant-based library of Zinc database was done for the selected five proteins using docking approach followed by MM-GBSA calculations. The top five hit molecules were identified for each protein. Based on docking score, and binding interactions, the top two hit molecules for each protein were selected as promising molecules for the molecular dynamic (MD) simulation study with the five proteins. Therefore, from this in silico based study, we report that Mangiferin could be a potential molecule targeting Wnt signaling pathway modulating the LRP6 activity, Baicalin for AChE activity, Chebulic acid for DKK1, ZINC103539689 for WIF1, and Morin for GSk-3β protein. However, further validation of the activity is warranted based on in vivo and in vitro experiments for better understanding and strong claim. This study provides an in silico approach for the identification of modulators of the Wnt signaling pathway as a new therapeutic approach for AD.

Identification of Potential Antiviral Inhibitors from Hydroxychloroquine and 1,2,4,5-Tetraoxanes Analogues and Investigation of the Mechanism of Action in SARS-CoV-2

This study aimed to identify potential inhibitors and investigate the mechanism of action on SARS-CoV-2 ACE2 receptors using a molecular modeling study and theoretical determination of biological activity. Hydroxychloroquine was used as a pivot structure and antimalarial analogues of 1,2,4,5 tetraoxanes were used for the construction and evaluation of pharmacophoric models. The pharmacophore-based virtual screening was performed on the Molport^® database (~7.9 million compounds) and obtained 313 structures. Additionally, a pharmacokinetic study was developed, obtaining 174 structures with 99% confidence for human intestinal absorption and penetration into the blood-brain barrier (BBB); posteriorly, a study of toxicological properties was realized. Toxicological predictions showed that the selected molecules do not present a risk of hepatotoxicity, carcinogenicity, mutagenicity, and skin irritation. Only 54 structures were selected for molecular docking studies, and five structures showed binding affinity (ΔG) values satisfactory for ACE2 receptors (PDB 6M0J), in which the molecule MolPort-007-913-111 had the best ΔG value of -8.540 Kcal/mol, followed by MolPort-002-693-933 with ΔG = -8.440 Kcal/mol. Theoretical determination of biological activity was realized for 54 structures, and five molecules showed potential protease inhibitors. Additionally, we investigated the Mpro receptor (6M0K) for the five structures via molecular docking, and we confirmed the possible interaction with the target. In parallel, we selected the TopsHits 9 with antiviral potential that evaluated synthetic accessibility for future synthesis studies and in vivo and in vitro tests.

Balanced QSAR and Molecular Modeling to Identify Structural Requirements of Imidazopyridine Analogues as Anti-infective Agents Against Trypanosomiases

Human African trypanosomiasis (HAT), a fatal infection caused by Trypanosoma brucei (T. brucei) is considered as a neglected disease in the tropical areas, and newer agents with unique mechanism of action are urgently needed. In this work, 65 Imidazopyridine analogues from known literature were selected for building statistically robust genetic algorithm (GA) based QSAR models. Furthermore, values for the various cross-validation properties supported its statistical robustness (model 1, [Formula: see text], RMSE[Formula: see text], MAE[Formula: see text], CCC[Formula: see text], and [Formula: see text]). Our in silico ADMET analysis revealed that a designed molecule, S10 may act as potent lead (T. brucei, pEC[Formula: see text] ([Formula: see text]M), [Formula: see text]) with better pharmacokinetics, no carcinogenicity, class III acute oral toxicity, minimal OCT1 and OCT2 inhibitions and no eye corrosion profiles. Our molecular docking analysis (on 42 drug targets) for a dataset and designed molecules demonstrated higher binding affinity of Imidazopyridine analogues with T. brucei farnesyl diphosphate synthase (TbFPPS) (PDB id: 2I19). This observation was further supported by 100[Formula: see text]ns molecular dynamics analysis retaining better stability of complex. Thus, imidazopyridine analogues would provide a promising scaffold for the development of anti-HAT agents.

Newly Identified COVID-19 Drug Candidates Based on Computational Strategies

The COVID-19 has raised a public health catastrophe in early 2020 worldwide. Despite several approved vaccines that have repressed the pandemic and decreased the mortality rate since then, attempts to discover an effective antiviral drug have not indicated reliable results. In this research, in silico studies (virtual screening and molecular docking) were performed based on quinoline structure to identify novel drug candidates against SARS-CoV-2 before laboratory evaluations. A chemical library consisting of 548 compounds was collected from literature mining of five databases to select the best ligands interacting with three target proteins of SARS-CoV-2, including the main protease, spike protein, and chimeric receptor-binding domain in a complex of human angiotensin-converting enzyme 2. The top five compounds that presented suitable binding energy against each target protein are reported in detail for the first time. Notably, new compound N-4-(6-methyl-3-pyridinyl) phenyl)-9-acridinamine showed high affinity to all selected proteins. These identified compounds will help in speeding up the drug development against COVID-19.

Computational Approaches: Drug Discovery and Design in Medicinal Chemistry and Bioinformatics

To date, computational approaches have been recognized as a key component in drug design and discovery workflows [...].

Chemical Composition and Preliminary Toxicity Evaluation of the Essential Oil from Peperomia circinnata Link var. circinnata. (Piperaceae) in Artemia salina Leach

Peperomia Ruiz and Pav, the second largest genus of the Piperaceae, has over the years shown potential biological activities. In this sense, the present work aimed to carry out a seasonal and circadian study on the chemical composition of Peperomia circinata essential oils and aromas, as well as to evaluate the preliminary toxicity in Artemia salina Leach and carry out an in silico study on the interaction mechanism. The chemical composition was characterized by gas chromatography (GC/MS and GC-FID). In the seasonal study the essential oil yields had a variation of 1.2–7.9%, and in the circadian study the variation was 1.5–5.6%. The major compounds in the seasonal study were β-phellandrene and elemicin, in the circadian they were β-phellandrene and myrcene, and the aroma was characterized by the presence of β-phellandrene. The multivariate analysis showed that the period and time of collection influenced the essential oil and aroma chemical composition. The highest toxicity value was observed for the essential oil obtained from the dry material, collected in July with a value of 14.45 ± 0.25 μg·mL⁻¹, the in silico study showed that the major compounds may be related to potential biological activity demonstrated by the present study.

Vitex negundo L. Essential Oil: Odorant Binding Protein Efficiency Using Molecular Docking Approach and Studies of the Mosquito Repellent

Simple Summary

Malaria fever kills millions of people annually in the tropical and subtropical countries of Africa and Asia. Because there is no effective vaccine, malaria prevention is exclusively dependent on avoiding human-vector interaction. The interaction of Vitex negundo essential oil constituents with Anopheles gambiae Odorant Binding Proteins (OBP), as well as its compositional variation, repellent efficacy, and toxicity profile, are investigated in this work. The oils were subjected to GC-MS analysis, a mosquito behavioral test, OBP-ligand interactions, Anopheles species authentication, and toxicity profile. Docking protocol validation was achieved by redocking the co-crystallized ligands and root mean square deviation (RMSD) calculation. The oil yields and compositions are climate–soil dependent with ≈71.39% monoterpenes and ≈16.32% sesquiterpene. Optimal repellency is achieved at 15 min at ED₅₀ 0.08–0.48% v/v while the RMSD was estimated to be within 0.24–1.35 Å. Strong affinities, −6.4 to −5.4 kcal/mol, were demonstrated by α-pinene, citronellal, linalool, and myrcene for OBP1, OBP7, OBP4, and OBP. respectively. The hydrophobic interactions involve Leu17, Cys35, ALA52, Leu73, Leu76, Ala88, Met91, Lys93, Trp114, Phe123, and Leu124 receptors on α-helixes 1–7 within the binding cavities, and may block the olfactory receptors resulting in disorientation. α-pinene, linalool, and myrcene are safe and suitable for use in the development of green and innovative repellents because their ligand efficiency metrics, ADME/tox, and repellency screening are all within the threshold values.

Abstract

(1) Background: Malaria fever affects millions of people yearly in Africa and Asia’s tropical and subtropical areas. Because there is no effective vaccine, malaria prevention is solely dependent on avoiding human-vector interaction. (2) Aim: This study examines the interaction between the constituents of Vitex negundo essential oil and Anopheles gambiae Odorant Binding Proteins (OBP) as well as the compositional variation, repellent efficacy, and toxicity profile. (3) Methods: The oils were subjected to GC-MS and mosquito behavioral analysis. OBP–ligand interactions, Anopheles species authentication, and the toxicity profile were determined by molecular docking, PCR assay and in silico ADME/tox tool. Docking protocol validation was achieved by redocking the co-crystallized ligands into the protein binding pocket and root mean square deviation (RMSD) calculation. (4) Results: The oil yields and compositions are climate–soil dependent with ≈71.39% monoterpenes and ≈16.32% sesquiterpene. Optimal repellency is achieved at 15 min at ED₅₀ 0.08–0.48% v/v while the RMSD was estimated to be within 0.24–1.35 Å. Strong affinities were demonstrated by α-pinene (−6.4 kcal/mol), citronellal (−5.5 kcal/mol), linalool (−5.4 kcal/mol), and myrcene (−5.8 kcal/mol) for OBP1, OBP7, OBP4, and OBP; respectively. The hydrophobic interactions involve Leu17 (α-helix 1), Cys35 (α-helix 2), ALA52 (α-helix 3), Leu73, Leu76 (α-helix 4), Ala88, Met91, Lys93, Trp114 (α-helix 5), Phe123 (α-helix 6), and Leu124 (α-helix 7) receptors within the binding cavities, and may cause blocking of the olfactory receptors resulting in disorientation. (5) Conclusion: The ligand efficiency metrics, ADME/tox and repellency screening are within the threshold values; hence, α-pinene, linalool, and myrcene are safe and fit-to-use in the development of a green and novel repellent.

Selection of SARS-CoV-2 main protease inhibitor using structure-based virtual screening

Background: Conserved domains within SARS coronavirus 2 nonstructural proteins represent key targets for the design of novel inhibitors. Methods: The authors aimed to identify potential SARS coronavirus 2 NSP5 inhibitors using the ZINC database along with structure-based virtual screening and molecular dynamics simulation. Results: Of 13,840 compounds, 353 with robust docking scores were initially chosen, of which ten hit compounds were selected as candidates for detailed analyses. Three compounds were selected as coronavirus NSP5 inhibitors after passing absorption, distribution, metabolism, excretion and toxicity study; root and mean square deviation; and radius of gyration calculations. Conclusion: ZINC000049899562, ZINC000169336666 and ZINC000095542577 are potential NSP5 protease inhibitors that warrant further experimental studies.

Energy and reactivity profile and proton affinity analysis of rimegepant with special reference to its potential activity against SARS-CoV-2 virus proteins using molecular dynamics

Rimegepant is a new medicine developed for the management of chronic headache due to migraine. This manuscript is an attempt to study the various structural, physical, and chemical properties of the molecules. The molecule was optimized using B3LYP functional with 6-311G + (2d,p) basis set. Excited state properties of the compound were studied using CAM-B3LYP functional with same basis sets using IEFPCM model in methanol for the implicit solvent atmosphere. The various electronic descriptors helped to identify the reactivity behavior and stability. The compound is found to possess good nonlinear optical properties in the gas phase. The various intramolecular electronic delocalizations and non-covalent interactions were analyzed and explained. As the compound contain several heterocyclic nitrogen atoms, they have potential proton abstraction features, which was analyzed energetically. The most important result from this study is from the molecular docking analysis which indicates that rimegepant binds irreversibly with three established SARS-CoV-2 proteins with ID 6LU7, 6M03, and 6W63 with docking scores − 9.2988, − 8.3629, and − 9.5421 kcal/mol respectively. Further assessment of docked complexes with molecular dynamics simulations revealed that hydrophobic interactions, water bridges, and π–π interactions play a significant role in stabilizing the ligand within the binding region of respective proteins. MMGBSA-free energies further demonstrated that rimegepant is more stable when complexed with 6LU7 among the selected PDB models. As the pharmacology and pharmacokinetics of this molecule are already established, rimegepant can be considered as an ideal candidate with potential for use in the treatment of COVID patients after clinical studies.

One-Pot Synthesis of Coumarin-Indomethacin Hybrids as COX-2 Targeting Probes for Cancer Imaging

Facile synthesis of 6- or 7-substituted coumarin-indomathacin hybrids (Coum-IDM) has been developed for specific cyclooxygenase-2 (COX-2) binding along with their intrinsic fluorescent properties. A mild and rapid condensation/dehydrative cyclization of 2-hydroxy benzaldehyde with activated indomethacin was carried out in one step under ultrasound irradiation. Coum-IDM₄ was found to be the best of this series as it presented significant binding to COX-2 and exhibited higher fluorescent intensity in cancer cells than in normal cells. Therefore, in the light of drug development tools, this new hybrid system could be a potential targeted probe for COX-2-overexpressed inflammation and cancer-cell tracking.

First report on the Annona exsucca DC. Essential oil and in silico identification of potential biological targets of its major compounds

In the present study, the essential oil (EO) of Annona exsucca DC. or Rollinia exsucca was extracted by hydrodistillation, and the identification and quantification of volatile compounds were performed by GC-MS and GC-FID. A. exsucca leaves were collected from the Magalhães Barata, northeast of the State of Pará (Brazil) in March and September of 2019. Moreover, we used computational approaches to evaluate possible biological targets for the major compounds of the EO. In the sample obtained in March, 50 compounds were identified, with hydrocarbon sesquiterpenes being the predominant ones with the content of 80.52%. In the sample collected in September, 58 compounds were identified, and the chemical class of hydrocarbon monoterpenes and sesquiterpenes were the dominant ones with contents of 43.36 and 31.29%, respectively. Computational methods demonstrated that some major compounds have potential biological activity against some strains of pathogenic bacteria, as well as against molecular targets involved in cancer development.

Extraction Yield, Chemical Composition, Preliminary Toxicity of Bignonia nocturna (Bignoniaceae) Essential Oil and in Silico Evaluation of the Interaction

Bignonia nocturna (Bignoniaceae) is a plant used for medicinal purposes by the Amazonian indigenous peoples. To date, there have been no reported studies on its toxicity. The present study aimed to evaluate the chemical composition of essential oils obtained from Bignonia nocturna by different extraction techniques. In addition, an in silico study of the molecular interactions was performed using molecular docking and molecular dynamics. The extractions were carried out by hydrodistillation, simultaneous distillation-extraction, and steam distillation, using samples collected from the Amazon in summer and winter. The chemical composition was analyzed by GC/FID and GC/MS, and the cytotoxic activity in Artemia salina Leach was evaluated. The maximum yield (1.38 % w/w) was obtained by hydrodistillation. The results indicated that benzaldehyde predominated in all the fractions of both the volatile concentrate and the essential oils. In addition, the oil proved to be highly toxic to Artemia salina. The computer simulation results indicated that benzaldehyde strongly interacts with acetylcholinesterase, which is the likely interaction mechanism responsible for the cytotoxicity.

Identification of novel potential cyclooxygenase-2 inhibitors using ligand- and structure-based virtual screening approaches

Cyclooxygenase 2 (COX-2) is a well-established target for the design of anti-inflammatory intermediates. Celecoxib was selected as a template molecule to perform ligand-based virtual screening, i.e. to search for structures with similarity in shape and electrostatic potential, with a gradual increase in accuracy through the combined fitting of several steps using eight commercial databases. The molecules ZINC408709 and ZINC2090319 reproduced values within the limits established in an initial study of absorption and distribution in the body. No alert was fired for possible toxic groups when these molecules were subjected to toxicity prediction. Molecular docking results with these compounds showed a higher binding affinity in comparison to rofecoxib for the COX-2 target. Additionally, ZINC408709 and ZINC2090319 were predicted to be potentially biologically active. In in silico prediction of endocrine disruption potential, it was established that the molecule ZINC2090319 binds strongly to the target related to cardiovascular risk in a desirable way as a non-steroidal antagonist and ZINC408709 binds strongly to the target that is associated with the treatment of inflammatory pathologies and similar to celecoxib. Metabolites generated from these compounds are less likely to have side effects. Simulations were used to evaluate the interaction of compounds with COX-1 and COX-2 during 200 ns. Despite the differences, ZINC408709 molecule showed better stability for COX-2 during molecular dynamics simulation. In the calculations of free energy MM/PBSA, the molecule ZINC408709 ΔGbind value has a higher affinity to celecoxib and rofecoxib COX-2. This demonstrates that the selected substances can be considered as promising COX-2 inhibitors. Communicated by Ramaswamy H. Sarma.