Lipinski Filter Research Articles

Cheminformatic evaluation of the multi-protein binding potential of some diselenide derivatives: A plausible drug discovery approach for leishmaniasis

Over twelve million individuals worldwide suffer from leishmaniasis, and an additional billion people are at risk in places where the disease is prevalent. This work was motivated by the lack of vaccination against leishmaniasis and the shortcomings of current anti-leishmanial treatments. Large compound libraries can be screened using computational methods, which can also be used to analyze pharmacokinetic features, explore protein–ligand interactions, and quickly, accurately, and precisely create novel pharmacological entities. Virtual docking screening was performed to assess the multi-protein targeting capability of certain diselenides using four Leishmania protein targets—2XOX, 3SPX, 5ZWY, and 6K91. Following the Lipinski filter's screening of a subset of analogues, density functional theory (DFT), molecular dynamics (MD) simulation analysis, and ADMET profiles were used to profile the lead compounds. The overall average binding affinity of ligands to target proteins is as follows: 3SPX (− 184.998 kcal/mol) > 6K91 (− 180.114 kcal/mol) > 2XOX (− 176.581 kcal/mol) > 5ZWY (− 157.198 kcal/mol). The focus is on ligands that target all investigated proteins with binding scores greater than the average binding scores for the proteins as a whole for which seven compounds were identified that also showed higher MolDock scores than both reference drugs (Miltefosine and Pentamidine). Further screening showed four compounds (4, 7, 25, and 26) passed Lipinski’s test, making them orally bioavailable with excellent ADMET properties that compared well to both reference medications. The DFT analysis and MD simulation results indicate these compounds' favorability, stability, and reactivity in binding to the studied targets, 3SPX and 6K91 with 25_3SPX and 4_6K91 showing the highest binding free energy (MM-GBSA) of − 88.35 kcal/mol and − 90.29 kcal/mol respectively. Conclusively, the chosen diselenides could be developed as prospective anti-leishmanial pharmacological compounds or as useful scaffolds for creating more potent anti-leishmanial drugs.

Discovery of Potential Inhibitors of CDK1 by Integrating Pharmacophore-Based Virtual Screening, Molecular Docking, Molecular Dynamics Simulation Studies, and Evaluation of Their Inhibitory Activity.

The ability of CDK1 to compensate for the absence of other cell cycle CDKs poses a great challenge to treat cancers that overexpress these proteins. Despite several studies focusing on the area, there are no FDA-approved drugs selectively targeting CDK1. Here, the study aimed to develop potential CDK1 selective inhibitors through drug repurposing and leveraging the structural insights provided by the hit molecules generated. Approximately 280,000 compounds from DrugBank, Selleckchem, Otava and an in-house library were screened initially based on fit values using 3D QSAR pharmacophores built for CDK1 and subsequently through Lipinski, ADMET, and TOPKAT filters. 10,310 hits were investigated for docking into the binding site of CDK1 determined using the crystal structure of human CDK1 in complex with NU6102. The best 55 hits with better docking scores were further analyzed, and 12 hits were selected for 100 ns MD simulations followed by binding energy calculations using the MM-PBSA method. Finally, 10 hit molecules were tested in an in vitro CDK1 Kinase inhibition assay. Out of these, 3 hits showed significant CDK1 inhibitory potential with IC50 < 5 μM. These results indicate these compounds can be used to develop subtype-selective CDK1 inhibitors with better efficacy and reduced toxicities in the future.

Computational insights into the inhibitory mechanism of type 2 diabetes mellitus by bioactive components of Oryza sativa L. indica (black rice).

Type 2 diabetes mellitus is a metabolic disease categorized by hyperglycemia, resistance to insulin, and ß-cell dysfunction. Around the globe, approximately 422 million people have diabetes, out of which 1.5million die annually. In spite of innovative advancements in the treatment of diabetes, no biological drug has been known to successfully cure and avert its progression. Thereupon, natural drugs derived from plants are emerging as a novel therapeutic strategy to combat diseases like diabetes. The current study aims to investigate the antidiabetic potential of natural compounds of Oryza sativa L. indica (black rice) in disease treatment. Antioxidant activity and alpha amylase assays were performed to evaluate the therapeutic potential of the extract of Oryza sativa L. indica. Gas chromatography-mass spectrometry (GC-MS) was used for identification of constituents from the ethanol extract. ADMET profiling (absorption, distribution, metabolism, excretion, and toxicity), network pharmacology, and molecular dynamics simulation were employed in order to uncover the active ingredients and their therapeutic targets in O. sativa L. indica against type 2 diabetes mellitus. GC-MS of the plant extract provided a list of 184 compounds. Lipinski filter and toxicity parameters screened out 18 compounds. The topological parameters of the protein-protein interaction (PPI) were used to shortlist the nine key proteins (STAT3, HSP90AA1, AKT1, SRC, ESR1, MAPK1, NFKB1, EP300, and CREBBP) in the type 2 diabetes mellitus pathways. Later, molecular docking analysis and simulations showed that C14 (1H-purine-8-propanoic acid, .alpha.-amino-2, 3, 6, 7-tetrahydro-1,3,7-trimethyl-2,6-dioxo-) and C18 (cyclohexane-carboxamide, N-furfuryl) bind with AKT1 and ESR1 with a binding energy of 8.1, 6.9, 7.3, and 7.2kcal/mol, respectively. RMSD (root-mean-square deviation) and RMSF (root-mean-square fluctuation) values for AKT1 and ESR1 have shown very little fluctuation, indicating that proteins were stabilized after ligand docking. This study suggests therapeutic drug candidates against AKT1 and ESR1 to treat type 2 diabetes mellitus. However, further wet-lab analysis is required to discover the best remedy for type 2 diabetes mellitus.

Natural product-derived ALK inhibitors for treating ALK-driven lung cancers: an in silico study.

Anaplastic lymphoma kinase (ALK)-driven lung cancer represents a critical therapeutic target, demanding innovative approaches for the identification of effective inhibitors. Anaplastic lymphoma kinase (ALK), a key protein involved in the pathogenesis of ALK-driven lung cancers, has been the focus of extensive drug discovery efforts. This study employed a comprehensive computational drug discovery approach, integrating virtual screening with the Lipinski filter, re-docking, molecular dynamics (MD) simulations, and free energy calculations to identify potential inhibitors from a natural compound library. Utilizing the MTiOpenScreen web server, we screened for compounds that exhibit favorable interactions with ALK, resulting in 1227 compounds with virtual screening scores ranging from -10.2 to -3.7kcal/mol. Subsequent re-docking of three selected compounds (ZINC000059779788, ZINC000043552589, and ZINC000003594862) and one reference compound against ALK yielded docking scores -10.4, -10.2, -10.2, and -10.1kcal/mol, respectively. These compounds demonstrated promising interactions with ALK, suggesting potential inhibitory effects. Advanced analyses, including MD simulation and binding free energy calculations, further supported the potential efficacy of these compounds. MD simulations, particularly the root mean square deviation (RMSD) and root mean square fluctuation (RMSF) analyses, revealed that compounds ZINC000059779788 and ZINC000003594862 achieved better stability compared to compound ZINC000043552589. These stable conformations suggest effective binding over time. Free energy calculations using the MM/GBSA method showed that ZINC000059779788 had the most favorable binding energy, indicating a strong and stable interaction with the ALK protein. The promising computational findings from this study emphasize the necessity for additional experimental testing to verify the therapeutic efficacy of these natural compounds for treating lung cancers.

In Silico Investigation against Inhibitors of Alpha-Amylase Using Structure-based Screening, Molecular Docking, and Molecular Simulations Studies.

Type-II diabetes mellitus is a chronic disorder that results from fluctuations in the glucose level leading to hyperglycemia with severe adverse effects increasing worldwide. Alpha-Amylase is the key enzyme involved in the mechanism of glucose formation therefore Alpha-Amylase inhibitors have become a therapeutic target in the development of new leads as they have the potential to suppress glucose levels. Existing drugs targeting Alpha-Amylase highlight major drawbacks in terms of poor absorption rate that causes several gastrointestinal issues. So, this research is aimed to develop novel inhibitors interacting with Alpha-Amylase's active site using structural-based screening, binding pattern analysis, and molecular dynamic simulation. Hence, to search for a potential lead, we analyzed a total of 133 valiolamine derivatives and 535 desoxynojirimycin derivatives that exhibited drug-like properties screened through Lipinski filters. Virtual screening followed by binding interaction analysis we identified ten compounds that exhibited better binding energy scores compared to the standard drugs voglibose and miglitol, used in our study. The docking analysis, ADMET and metabolic site prediction estimated the best top two compounds with good drug profiles. Further, top compounds VG9 and VG15 were promoted to simulation study using the Biovia Discovery study to access the stability at a time interval of 100 ns. MD simulation results revealed that our compound VG9 possesses better conformational stability in the complex to the active site residues of Alpha-Amylase target protein than standard drug voglibose. Thus, our investigation revealed that compound VG9 also exhibits the best pharmacokinetic as well as binding affinity results and could act as a potential lead compound targeting Alpha-Amylase for Type II diabetes.

Modeling Hexaazacylcododeca Metal Complexes as a Radical Trapping Antioxidant: Prospects as a Potential Drug

AbstractFree radicals produced due to the disturbance in homeostasis bring about oxidative stress causing various diseases. This oxidative stress can be prevented by using antioxidants. In this article, a hexaazacylcododeca copper complex is reported as a radical‐trapping antioxidant (RTA). A detailed mechanistic study suggests that the designed complex is capable of trapping six radicals. The study confirms Path 6 as the most probable pathway, which is the radical addition to the ethene moiety of the complex. Moreover, it has a lower N−H bond dissociation enthalpy (BDE) than the recently reported bis(thiosemicarbazone) copper complex suggesting it could be a better antioxidant. In addition, the effect of different metals (Co, Fe, Pt, Ca, Ba, Sr, Au, Ag, Ni, and Zn) in their antiradical activity has been studied which suggests that among the studied metal complexes the Cu metal complex is the best metal complex for radical trapping. Further, the drug‐likeness is tested with the Lipinski filter along with the absorption, distribution, metabolism, and excretion (ADME) properties. Lastly, docking analysis tested against proteins responsible for ferroptosis shows that the modeled RTA can inhibit such diseases. Thus, it can be proposed that the designed RTA is a potential drug candidate.

Synthesis, Anticancer Activity, and In Silico Modeling of Alkylsulfonyl Benzimidazole Derivatives: Unveiling Potent Bcl-2 Inhibitors for Breast Cancer.

A series of alkylsulfonyl 1H-benzo[d]imidazole derivatives were synthesized and evaluated for anticancer activity against human breast cancer cells, MCF-7 in vitro. The cytotoxic potential was determined using the xCELLigence real-time cell analysis, and expression levels of genes related to microtubule organization, tumor suppression, apoptosis, cell cycle, and proliferation were examined by quantitative real-time polymerase chain reaction. Molecular docking against Bcl-2 was carried out using AutoDock Vina, while ADME studies were performed to predict the physicochemical and drug-likeness properties of the synthesized compounds. The results revealed that compounds 23 and 27 were the most potent cytotoxic derivatives against MCF-7 cells. Gene expression analysis showed that BCL-2 was the most prominent gene studied. Treatment of MCF-7 cells with compounds 23 and 27 resulted in significant downregulation of the BCL-2 gene, with fold changes of 128 and 256, respectively. Docking analysis predicted a strong interaction between the compounds and the target protein. Interestingly, all of the compounds exhibit a higher binding affinity toward Bcl-2 than the standard drug (compound 27 vina score = -9.6 kcal/mol, vincristine = -6.7 kcal/mol). Molecular dynamics simulations of compounds 23 and 27 showed a permanent stabilization in the binding site of Bcl-2 for 200 ns. Based on Lipinski and Veber's filters, all synthesized compounds displayed drug-like characteristics. These findings suggest that compounds 23 and 27 were the most promising cytotoxic compounds and downregulated the expression of the BCL-2 gene. These derivatives could be further explored as potential candidates for the treatment of breast cancer.

Structure-based Virtual Screening, Molecular Docking, Molecular Dynamics Simulation, and Metabolic Reactivity studies of Quinazoline Derivatives for their Anti-EGFR Activity Against Tumor Angiogenesis

Epidermal growth factor receptor (EGFR/HER-1) and its role in tumor development and progression through the mechanism of tumor angiogenesis is prevalent in non-small lung cancer, head and neck cancer, cholangiocarcinoma & glioblastoma. Previous treatments targeting the oncogenic activity of EGFR's kinase domain have been hindered by acquired mutational resistance and side effects from existing drugs like erlotinib, highlighting the need for new EGFR inhibitors through structure- based drug designing The research aims to develop novel quinazoline derivatives through structure-based virtual screening, molecular docking, and molecular dynamics simulation to potentially interact with EGFR's kinase domain and impede tumor angiogenic phenomenon. Quinazoline derivatives were retrieved and filtered from the PubChem database using structure- based virtual screening and the Lipinski rule of five drug-likeness studies. Molecular docking-based virtual screening methods and molecular dynamics simulation were then carried out to identify top leads A total of 1000 quinazoline derivatives were retrieved, with 671 compounds possessing drug-- like properties after applying Lipinski filters. Further filtration using ADME and toxicity filters yielded 28 compounds with good pharmacokinetic profiles. Docking-based virtual screening identified seven compounds with better binding scores than the control drug, dacomitinib. After cross-checking binding scores, three top compounds QU524, QU571, and QU297 were selected for molecular dynamics simulation study of 100 ns interval using Desmond module of Schrodinger maestro to understand their conformational stability The research results showed that the selected quinazoline leads exhibited better binding affinity and conformational stability than the control drug, erlotinib. These compounds also had good pharmacokinetic and pharmacodynamic profiles and did not violate Lipinski’s rule of five limits. The findings suggest that these leads have the potential to target EGFR's kinase domain and inhibit the EGFR-associated phenomenon of tumor angiogenesis.

Lead generation of UPPS inhibitors targeting MRSA: Using 3D-QSAR pharmacophore modeling, virtual screening, molecular docking, and molecular dynamic simulations

Undecaprenyl Pyrophosphate Synthase (UPPS) is a vital target enzyme in the early stages of bacterial cell wall biosynthesis. UPPS inhibitors have antibacterial activity against resistant strains such as MRSA and VRE. In this study, we used several consecutive computer-based protocols to identify novel UPPS inhibitors. The 3D QSAR pharmacophore model generation (HypoGen algorithm) protocol was used to generate a valid predictive pharmacophore model using a set of UPPS inhibitors with known reported activity. The developed model consists of four pharmacophoric features: one hydrogen bond acceptor, two hydrophobic, and one aromatic ring. It had a correlation coefficient of 0.86 and a null cost difference of 191.39, reflecting its high predictive power. Hypo1 was proven to be statistically significant using Fischer’s randomization at a 95% confidence level. The validated pharmacophore model was used for the virtual screening of several databases. The resulting hits were filtered using SMART and Lipinski filters. The hits were docked into the binding site of the UPPS protein, affording 70 hits with higher docking affinities than the reference compound (6TC, − 21.17 kcal/mol). The top five hits were selected through extensive docking analysis and visual inspection based on docking affinities, fit values, and key residue interactions with the UPPS receptor. Moreover, molecular dynamic simulations of the top hits were performed to confirm the stability of the protein–ligand complexes, yielding five promising novel UPPS inhibitors.Graphical

Structural and Dynamical Basis of VP35-RBD Inhibition by Marine Fungi Compounds to Combat Marburg Virus Infection.

The Marburg virus (MBV), a deadly pathogen, poses a serious threat to world health due to the lack of effective treatments, calling for an immediate search for targeted and efficient treatments. In this study, we focused on compounds originating from marine fungi in order to identify possible inhibitory compounds against the Marburg virus (MBV) VP35-RNA binding domain (VP35-RBD) using a computational approach. We started with a virtual screening procedure using the Lipinski filter as a guide. Based on their docking scores, 42 potential candidates were found. Four of these compounds-CMNPD17596, CMNPD22144, CMNPD25994, and CMNPD17598-as well as myricetin, the control compound, were chosen for re-docking analysis. Re-docking revealed that these particular compounds had a higher affinity for MBV VP35-RBD in comparison to the control. Analyzing the chemical interactions revealed unique binding properties for every compound, identified by a range of Pi-cation interactions and hydrogen bond types. We were able to learn more about the dynamic behaviors and stability of the protein-ligand complexes through a 200-nanosecond molecular dynamics simulation, as demonstrated by the compounds' consistent RMSD and RMSF values. The multidimensional nature of the data was clarified by the application of principal component analysis, which suggested stable conformations in the complexes with little modification. Further insight into the energy profiles and stability states of these complexes was also obtained by an examination of the free energy landscape. Our findings underscore the effectiveness of computational strategies in identifying and analyzing potential inhibitors for MBV VP35-RBD, offering promising paths for further experimental investigations and possible therapeutic development against the MBV.

Computational Studies of Multi-Target Directed Ligands Against Acetylcholinesterase, Butyrylcholinesterase and Amyloid Beta as Potential Anti-Alzheimer’s Agents

The designed flavone-hydroxypyridinone derivatives were screened in silico with the multiple targets of Alzheimer’s disease (AD) for their binding affinity. In this study, 29 novel derivatives of flavone-hydroxypyridinone were docked with acetylcholinesterase, butyrylcholinesterase and amyloid beta to determine their binding interactions on these targets of AD. The designed ligands were passed through the Lipinski and Veber filter, of which 29 ligands (8 from series 1 and 21 from series 2) obeyed the rule. All the molecules were docked with all the targets. To refine and confirm the docking study results, the stability of complexes is verified using molecular dynamics simulations. As our aim is to develop Multi-Target Direct Ligand (MTDL), one ligand from both the series has been selected as MTDL, is one of the best-docked ligands, which interacts with the protein through hydrogen bond, Vander Waal interactions, [Formula: see text]-[Formula: see text] stacking and [Formula: see text]-alkyl interactions. Where amino acid residues such as Leu17, Lys16, Phe20 and Ala21 play important role in receptor–ligand interactions. The studies imply that the best-docked MTDL complex has a good binding affinity which has been further confirmed by molecular dynamic simulations and different pharmacokinetics parameters calculated. The study provides guidance for the development of flavone-hydroxypyridinone derivatives as MTDL against AD.

Unveiling Neuroprotective Potential of Spice Plant-Derived Compounds against Alzheimer's Disease: Insights from Computational Studies.

Alzheimer's disease (AD) is a serious threat to the global health care system and is brought on by a series of factors that cause neuronal dysfunction and impairment in memory and cognitive decline. This study investigated the therapeutic potential of phytochemicals that belong to the ten regularly used spice plants, based on their binding affinity with AD-associated proteins. Comprehensive docking studies were performed using AutoDock Vina in PyRx followed by molecular dynamic (MD) simulations using AMBER 14. The docking study of the chosen molecules revealed the binding energies of their interactions with the target proteins, while MD simulations were carried out to verify the steadiness of bound complexes. Through the Lipinski filter and admetSAR analysis, the chosen compounds' pharmacokinetic characteristics and drug likeness were also examined. The pharmacophore mapping study was also done and analyzed for best selected molecules. Additionally, principal component analysis (PCA) was used to examine how the general motion of the protein changed. The results showed quercetin and myricetin to be potential inhibitors of AChE and alpha-amyrin and beta-chlorogenin to be potential inhibitors of BuChE, exhibiting best binding energies comparable to those of donepezil, used as a positive control. The multiple descriptors from the simulation study, root mean square deviation (RMSD), root mean square fluctuation (RMSF), hydrogen bond, radius of gyration (Rg), and solvent-accessible surface areas (SASA), confirm the stable nature of the protein-ligand complexes. Molecular mechanic Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculations indicated the energetically favorable binding of the ligands to the protein. Finally, according to pharmacokinetic properties and drug likeness, characteristics showed that quercetin and myricetin for AChE and alpha-amyrin and beta-chlorogenin for BuChE were found to be the most effective agents for treating the AD.

Designing of Anticancer Therapeutical Strategies: Implications of Molecular Docking Studies of Phytochemicals of Cichorium Intybus to Metabolic Regulatory Enzymes

Background: Altered metabolism is a significant characteristic of cancer, with malignant cells exhibiting elevated levels of enzymes involved in bioenergetic and biosynthetic processes. Targeting metabolic enzymes has become a key approach in anticancer therapy, leading to the discovery of metabolic inhibitors such as 3-bromopyruvate (3-BP) with broad anticancer activity. Novel therapeutics are needed to treat and prevent this fatal disease, and natural substances are gaining attention as potentially safer alternatives to conventional therapies like chemotherapy. Methods: This study aimed to identify novel drug-like molecules for anticancer treatment using an in-silico approach. Twenty-eight phytocompounds from Cichorium intybus were selected for molecular docking against target enzymes involved in the TCA and glycolysis cycles and compared with 3-BP, a standard broad-spectrum anticancer drug, using Maestro (Schrodinger software). Results: Comparison of docking scores revealed that the phytoconstituents of Cichorium intybus exhibited stronger binding to metabolic enzymes compared to 3-BP. Additionally, drug-likeness analysis using the admetSAR and Lipinski filter indicated that most of the selected phytoconstituents and 3-BP demonstrated desirable criteria as anticancer drugs. Conclusion: Conclusion This research offers insightful information about molecular interactions between phytoconstituents of Cichorium intybus, 3-BP, and metabolic enzymes. These findings may contribute to the development and optimization of therapeutic approaches against cancer, utilizing these phytoconstituents as ligands.

Exploration of Novel PDEδ Inhibitor Based on Pharmacophore and Molecular Docking against KRAS Mutant in Colorectal Cancer.

The prenyl-binding protein, phosphodiesterase-δ (PDEδ), is essential for the localization of prenylated KRas to the plasma membrane for its signaling in cancer. The general objective of this work was to develop virtually new potential inhibitors of the PDEδ protein that prevent Ras enrichment at the plasma membrane. All computational molecular modeling studies were performed by Molecular Operating Environment (MOE). In this study, sixteen crystal structures of PDEδ in complex with fifteen different fragment inhibitors were used in the protein-ligand interaction fingerprints (PLIF) study to identify the chemical features responsible for the inhibition of the PDEδ protein. Based on these chemical characteristics, a pharmacophore with representative characteristics was obtained for screening the BindingDB database. Compounds that matched the pharmacophore model were filtered by the Lipinski filter. The ADMET properties of the compounds that passed the Lipinski filter were predicted by the Swiss ADME webserver and by the ProTox-II-Prediction of Toxicity of Chemicals web server. The selected compounds were subjected to a molecular docking study. In the PLIF study, it was shown that the fifteen inhibitors formed interactions with residues Met20, Trp32, Ile53, Cys56, Lys57, Arg61, Gln78, Val80, Glu88, Ile109, Ala11, Met117, Met118, Ile129, Thr131, and Tyr149 of the prenyl-binding pocket of PDEδ. Based on these chemical features, a pharmacophore with representative characteristics was composed of three bond acceptors, two hydrophobic elements, and one hydrogen bond donor. When the pharmacophore model was used in the virtual screening of the Binding DB database, 2532 compounds were selected. Then, the 2532 compounds were screened by the Lipinski rule filter. Among the 2532 compounds, two compounds met the Lipinski's rule. Subsequently, a comparison of the ADMET properties and the drug properties of the two compounds was performed. Finally, compound 2 was selected for molecular docking analysis and as a potential inhibitor against PDEδ. The hit found by the combination of structure-based pharmacophore generation, pharmacophore- based virtual screening, and molecular docking showed interaction with key amino acids in the hydrophobic pocket of PDEδ, leading to the discovery of a novel scaffold as a potential inhibitor of PDEδ.

Establishing the Role of Iridoids as Potential Kirsten Rat Sarcoma Viral Oncogene Homolog G12C Inhibitors Using Molecular Docking; Molecular Docking Simulation; Molecular Mechanics Poisson-Boltzmann Surface Area; Frontier Molecular Orbital Theory; Molecular Electrostatic Potential; and Absorption, Distribution, Metabolism, Excretion, and Toxicity Analysis.

The RAS gene family is one of the most frequently mutated oncogenes in human cancers. In KRAS, mutations of G12D and G12C are common. Here, 52 iridoids were selected and docked against 8AFB (KRAS G12C receptor) using Sotorasib as the standard. As per the docking interaction data, 6-O-trans-p-coumaroyl-8-O-acetylshanzhiside methyl ester (dock score: -9.9 kcal/mol), 6'-O-trans-para-coumaroyl geniposidic acid (dock score: -9.6 kcal/mol), 6-O-trans-cinnamoyl-secologanoside (dock score: -9.5 kcal/mol), Loganic acid 6'-O-beta-d-glucoside (dock score: -9.5 kcal/mol), 10-O-succinoylgeniposide (dock score: -9.4), Loganic acid (dock score: -9.4 kcal/mol), and Amphicoside (dock score: -9.2 kcal/mol) showed higher dock scores than standard Sotorasib (dock score: -9.1 kcal/mol). These common amino acid residues between iridoids and complexed ligands confirmed that all the iridoids perfectly docked within the receptor's active site. The 100 ns MD simulation data showed that RMSD, RMSF, radius of gyration, and SASA values were within range, with greater numbers of hydrogen bond donors and acceptors. MM/PBSA analysis showed maximum binding energy values of -7309 kJ/mol for 6-O-trans-p-coumaroyl-8-O-acetylshanzhiside methyl ester. FMO analysis showed that 6-O-trans-p-coumaroyl-8-O-acetylshanzhiside methyl ester was the most likely chemically reactive molecule. MEP analysis data highlighted the possible electrophilic and nucleophilic attack regions of the best-docked iridoids. Of all the best-docked iridoids, Loganic acid passed Lipinski, Pfizer, and GSK filters with a similar toxicity profile to Sotorasib. Thus, if we consider these iridoids to be KRAS G12C inhibitors, they will be a boon to mankind.

Synthesis, In-silico and In-vitro Antimycobacterial Studies on Novel Benzofuran Derivatives

Background: Benzofurans, an interesting heterocyclic compound, are available abundantly in nature and show a wider range of pharmacological activities. Moreover, in recent years this moeity has been found to have strong antituberculosis potential. Considering the importance of this moiety in the field of medicinal chemistry, we have synthesized a few benzofuran derivatives. Methods: These derivatives were also characterized by standard spectroscopic methods. Synthesized compounds were observed for their anti-tuberculosis activity using microplate Alamar Blue assay (MABA) assay and found to have a minimum of 100 (μg/mL) of minimum inhibitory concentration (MIC) values. Moreover, our molecular docking analyses depicted strong inhibitory potential against a popular TB target, Decaprenylphosphoryl-β-d-ribose 2′-epimerase (DprE1), a crucial enzyme for cell wall synthesis. Results: Compound 9e was found to have a strong binding energy score of -148.47 kcal/mol against the selected targets (PDB id: 6HEZ). Conclusion: All compounds were also found to possess drug-likeness characteristics when checked with Lipinski's filter.

In silico Exploration of Phytochemical based Thiazolidinone- Caffeic Acid- Indole New Chemical Entities for Simultaneous Management of Diabetes and Hypertension- A Fascinating Study.

Past few decades have witnessed the co-existence of diabetes and hypertension leading to other health disorders. Hence, it is imperative to look into new therapies for the treatment of both hypertension and diabetes simultaneously in order to gradually reduce the pill burden and subsequent side effects. The goal of the current work was to use several in silico methods to develop new entities that have both anti-diabetic and anti-hypertensive activity. Structure activity relationship was drawn from the literature considering Thiazolidinones (Anti diabetes), Indole (Antihypertensive) and naturally occurring polyphenols (Dual activity) for simultaneous management of hypertension and diabetes. Fifty-six new chemical entities were designed and subjected to ADME and docking studies. Based on the Lipinski filter, bioavailability and lead likeness nineteen molecules were further docked into three PDB's (5Y2T, 4BVN, 1O8A). The majority of the NCE's have shown higher binding affinities than the standard drugs, with Compound 42 having the best results. Among nineteen NCE's, 50% of the compounds have shown the involvement of Thiazolidinone, Indole and Catechol pharmacophores with prominent hydrogen bonds, hydrophobic, electrostatic and pi-pi stacking interactions with all three PDB's signifying their potential dual activity. Most favourable interactions were shown by compound 42. The results obtained are encouraging for further exploration of the hit molecules for simultaneous treatment of the two diseases.

Molecular Docking and Analysis of some Ligands on Var2csA Target

Purpose: Prevalence of malaria during pregnancy and the spate of drug resistance by malaria parasites have constantly impacted maternal, perinatal and neonatal outcomes, especially in sub-Saharan Africa. This study aims to discover “in silico” non-recombinant molecules which can interact with placental chondroitin sulfate to inhibit binding or displace bound var2csA from the placenta in order to prevent pregnancy associated malaria.&#x0D; Methodology: Protein data bank (rcsb.org) and PubChem were used to download the chemical structures of the receptor (3bqk) and those of the ligands. Canonical SMILES and other information about the ligands and the receptor were extracted from PubChem. Toxtree, Toxicity Estimation Software Tool (TEST), SwissADMET, Molinspiration and Lazar Toxicity Predicter were employed to test various toxicity and safety parameters of lead compounds. The structure of the macromolecule – chondroitin sulfate A (CSA) was retrieved by searching in the protein data bank (PDB) (rcsb.org/structure/3bqk); downloaded, and saved as a PDB format.&#x0D; Findings: Molecular modeling and toxicity predictors used in this study indicated that among the ligands screened, IH3 had the lowest binding energy of -9.8Kcal/mol while var2csA had -2.8Kcal/mol. Var2csA is parasite’s adhesive protein. It was also observed that out of the 90 ligands (binding affinity range -9.8 to -1.0 Kcal/mol) screened, IH3 (-9.8Kcal/mol), FAD (-8.4 Kcal/mol), NDP (-8.2 Kcal/mol), A5A (-8.2 Kcal/mol), ABO (-8.1 Kcal/mol), IH2 (-7.8 Kcal/mol), 2RT (-7.7 Kcal/mol), CRO (-7.7 Kcal/mol) and IH1 (-7.7 Kcal/mol) appear to be the most promising lead compounds to occupy var2csA binding pocket in pCSA in order to prevent adhesion of malaria infected erythrocytes to the placenta. SwissADME and Molinspiration Cheminformatics for LogP (mean of 1.07 and range of -2.79 to 4.18) of the lead compounds showed no correlations between lipophilicity and interaction with receptors. Of all the compounds selected for analysis, only ABO and 2RT exhibited drug-like properties based on Ghose, Lipinski and Veber filters.&#x0D; Conclusion: Data obtained from the study therefore suggests that IH3, FAD, NDP, A5A, ABO, IH2, 2RT, CRO, IH1 and var2csA make favourable lead candidates for targeting pCSA and therefore require further in vitro and in vivo evaluations.&#x0D; Recommendation: This study therefore recommends the repurposing and extending the use of flavin adenine dinucleotide (FAD) to cover prophylactic management of malaria among pregnant women.

Design, synthesis and evaluation of novel Se-alkylated pyrazoles and their cyclized analogs as potential anticancer agents

A simple multicomponent reaction (MCR) was utilized to synthesize a series of 5-alkylated selanyl-1H-pyrazole derivatives 3a-d, 6a-d, and their 4-amino-5-substituted selenolo[2,3-c]pyrazole analogs (4a-d). The methodology is based on the substitution of selenium for the chlorine atom in the chloro pyrazole carbonitrile compound 1via reduction with sodium borohydride in a nitrogen atmosphere, followed by in-situ substitution reactions with various α-halo alkylating agents in the presence of a basic catalyst. The structures of the compounds were confirmed using elemental and spectroscopic techniques (FT-IR, 1H, 13C NMR, and mass spectrometry). The compounds were screened for their anticancer activity which showed promising results and compounds 4c and 6d exhibited the highest cytotoxicity against the HepG2 cell line with pIC50 values of 4.30 and 4.49 respectively, without showing any off-target toxicity. These molecules also, displayed good ADMET features, passed Lipinski's filters, showed good drug-likeness properties, and were predicted to be effective dual EGFR and VEGFR-2 inhibitors, causing downregulation of S100A4 and MMP-9 genes. Together, these results make these molecules as important lead molecules that could be studied further for their anticancer properties.

Isolation, Cytotoxicity Evaluation, Docking, ADMET and Drug Likeness Studies of Secondary Metabolites from the Stem Bark ofAnthocephalus cadamba(Roxb.)

AbstractPhytochemical investigation of the stem bark ofAnthocephalus cadamba(Rubiaceae) led to the isolation of total ten secondary metabolites (1‐10) including β–sitosterol (1), ursolic acid (2), vanillic acid (3), quinovic acid (4), 3‐O‐[α‐L‐rhamnopyranosyl]‐quinovic acid (5), β‐sitosterol β‐D‐glucoside (6), cadambine (7), 3β‐dihydrocadambine (8), 7‐O‐acetyl loganin (9) and hexylp‐coumarate (10). Four acetylated derivatives2 a,5 a,7 aand8 aobtained through acetylation of compounds2,5,7and8respectively. All the compounds characterized using1H and13CNMR, HRESIMS and IR and comparison with literature. Compound4showed the best cytotoxic activity with IC50value 4 and 7 μM against pancreatic (MIA‐pa‐Ca‐2) and leukemia (HL‐60) cancer cells respectively. Docking results supported the anticancer potential of compound4viainhibition of EGFR receptor (PDB ID:3POZ) and its pharmacokinetic profile found optimized as per the Lipinski's filter. Therefore compound4has the potential to be developed as an anticancer agent against pancreatic cancer cells.