Docking Score Research Articles

Investigation of Novel Quinoline Derivatives Targeting Epidermal Growth Factor Receptors as Anticancer Agents a Computational Approach

Background: Newer chemical entities are created and synthesis has been made feasible by a variety of computer-aided drug design (CAAD) techniques. In addition to facilitating the visualisation of the ligand-target binding process, the application of in silico methodologies and structure-based drug design (SBDD) allows for the prediction of receptor affinities and significant binding pocket locations. Objective: The goal of the current study was to identify new quinoline derivatives by computational methods specially designed to bind the EGFR receptor in the treatment of breast cancer. Materials and Methods: ChemAxon Marvin Sketch 5.11.5 was used to create derivatives of quinolines. The admetSAR online web tools and SwissADME were utilised to forecast the toxicity and pharmacokinetic characteristics of several substances. A multitude of software programmes, such as Autodock 1.1.2, MGL Tools 1.5.6, Procheck, Protparam ExPasy tool, PyMOL, and Biovia Discovery Studio Visualizer v20.1.0.19295 were also employed to ascertain the ligand-receptor interactions between quinoline derivatives and the target receptor (PDB -5GNK). Result: Almost all components were shown to be less hazardous, orally consumable and to have the appropriate pharmacokinetic characteristics based on in silico study. All newly generated derivative compounds have higher docking scores when compared to the widely used medication sorafenib. Conclusion: Interactions with quinoline analogues boost binding energy and the number of Hbonds produced, making them a suitable place to start when creating compounds for further exploration. The quinoline moiety increases its potential as a novel therapy alternative for breast cancer and could facilitate more comprehensive in vivo, in vitro, chemical-based, and pharma studies by medicinal chemists.

New series of 4,6-diaryl pyrimidines: facile synthesis and antiproliferative activity as dual EGFR/VEGFR-2 inhibitors

IntroductionWe developed and produced a new series of 4,6-diaryl-pyrimidines 9–29 as antiproliferative agents targeting EGFR/VEGFR-2.MethodsThe antiproliferative efficacy of the novel targets was assessed against a panel of 60 NCI cancer cell lines and four cancer cell lines in vitro.Results and DiscussionCompounds 14, 17, 19, 22, 25, and 29 demonstrated the greatest potency among the derivatives, with GI50 values between 22 and 33 nM; compounds 22 and 29 exhibited the highest potency, with GI50 values of 22 and 24 nM, respectively. We subsequently examined the most efficient derivatives as dual EGFR/VEGFR-2 inhibitors, finding that compounds 22 and 29 functioned as dual inhibitors. Moreover, 22 and 29 can act as apoptotic inducers by increasing Bax levels and decreasing levels of the anti-apoptotic protein Bcl2. At both 24- and 48-h intervals, the cell migration rates of compounds 22 and 29 were lower than those of untreated cells, according to the migration rate and wound closure percentage assessment. The wound closure rate reached 100% after 72 h of therapy with compound 22 but only 80% with compound 29. The docking study showed that compounds 22 and 29 had docking scores similar to those of Erlotinib and Sorafenib, co-crystallized ligands, for the EGFR and VEGFR-2 proteins. The experiments on lipophilicity showed that the new pyrimidines had a consistent result. This group of compounds has better biological activity in all the biological systems studied with low lipophilicity.

An Insight into the Repurposing of Phytoconstituents obtained from Delhi's Aravalli Biodiversity Park as Antifungal Agents.

The global prevalence of fungal infections is alarming in both the pre- and post- COVID period. Due to a limited number of antifungal drugs, there are hurdles in treatment strategies for fungal infections due to toxic potential, drug interactions, and the development of fungal resistance. All the antifungal targets (existing and newer) and pipeline molecules showing promise against these targets are reviewed. The objective was to predict or repurpose phyto-based antifungal compounds based on a dual target inhibition approach (Sterol-14-α- demethylase and HSP-90) using a case study. In pursuit of repurposing the phytochemicals as antifungal agents, a team of researchers visited Aravalli Biodiversity Park (ABP), Delhi, India, to collect information on available medicinal plants. From 45 plants, a total of 1149 ligands were collected, and virtual screening was performed using Schrodinger Suite 2016 software to get 83 hits against both the target proteins: Sterol-14-α-demethylase and HSP-90. After analysis of docking results, ligands were selected based on their interaction against both the target proteins and comparison with respective standard ligands (fluconazole and ganetespib). We have selected Isocarthamidin, Quercetin and Boeravinone B based on their docking score and binding interaction against the HSP-90 (Docking Score -9.65, -9.22 and -9.21, respectively) and 14-α-demethylase (Docking Score -9.19, -10.76 and -9.74 respectively). The docking protocol was validated and MM/GBSA studies depicted better stability of selected three ligands (Isocarthamidin, Quercetin, Boeravinone B) complex as compared to standard complex. Further, MD simulation studies were performed using the Desmond (67) software package version 2018-4. All the findings are presented as a case study for the prediction of dual targets for the repurposing of certain phytochemicals as antifungal agents.

Anti-allergic potentials of Ceriops decandra leaves in TDI-induced allergic mice: Comprehensive in-vivo and in-silico studies

BackgroundCeriops decandra is a mangrove plant, locally known as “Goran”. This plant has been traditionally used to treat hepatitis, liver disorders, ulcers, diarrhea, gastrointestinal disorders, hemorrhage, pain, inflammation etc. Here we investigated the safety and anti-allergic potential of C. decandra leaves. MethodThe toxicity was screened by mortality rate, and behavioral changes in mice. Anti-allergic activity test was conducted on TDI induced allergy model mice by assessing the common allergic symptoms such as sneezing, scratching, nasal score as well as total and differential WBC counts. HPLC-DAD analysis was used to determine the polyphenolic compounds in crude extract and performed in-silico molecular docking against four potential receptor molecules (Histamine H1, Histidine decarboxylate, Interleukin- 4 and 5). ResultsThe toxicity study of the extract on mice showed the innocuous nature of the plant even at the highest dose of 3000 mg/kg. In the anti-allergic assay, the leaf extract significantly (p<0.05) decreased the allergic symptoms along with the WBC counts in blood in a dose-dependent manner. The HPLC profile revealed the presence of six phenolic compounds (Catechin hydrate, Caffeic acid, Vanillic acid, Syringic acid, Rutin hydrate, p-coumarin). Among those Rutin hydrate, exhibited the best docking scores at all the targeted protein molecules and the highest binding affinity was (-9.8 kcal/mol) against Interleukin-5. ConclusionC. decandra is safe and rich in several polyphenolic compounds which are effective against allergic syndromes which could be an effective option for the management of allergic symptoms, although clinical studies are required to establish the herbal formulation.

In silico Evaluation of NO-Sartans against SARS-CoV-2.

Numerous clinical trials are currently investigating the potential of nitric oxide (NO) as an antiviral agent against coronaviruses, including SARS-CoV-2. Additionally, some researchers have reported positive effects of certain Sartans against SARS-CoV-2. Considering the impact of NO-Sartans on the cardiovascular system, we have compiled information on the general structure, synthesis methods, and biological studies of synthesized NOSartans. In silico evaluation of all NO-Sartans and approved sartans against three key SARS-CoV- -2 targets, namely Mpro (PDB ID: 6LU7), NSP16 (PDB ID: 6WKQ), and ACE-2 (PDB ID: 1R4L), was performed using MOE. Almost all NO-Sartans and approved sartans demonstrated promising results in inhibiting these SARS-CoV-2 targets. Compound 36 (CLC-1280) showed the best docking scores against the three evaluated targets and was further evaluated using molecular dynamics (MD) simulations. Based on our in silico studies, CLC-1280 (a Valsartan dinitrate) has the potential to be considered as an inhibitor of the SARS-CoV-2 virus. However, further in vitro and in vivo evaluations are necessary for the drug development process.

Design, Synthesis and Evaluation of Benzimidazole Derivatives as IL‐6 Inhibitors and Their Role in Rheumatoid Arthritis

ABSTRACTInterleukin‐6 (IL‐6) is a pleiotropic cytokine that plays a major role in the development of Rheumatoid Arthritis (RA). In the present study, benzimidazole and benzene sulfonyl scaffold were identified as pharmacophore by analysis of literature reports and novel small molecule IL‐6 inhibitors were designed. These were screened via docking with IL‐6 (PDB: 1ALU), then and through Lipinski's rule of 5. Based on docking score, 10 best compounds (4a–4e and 7a–7e) were selected for synthesis and evaluated for IL‐6 inhibitory activity in vitro. Compounds 4b and 7b showed the maximum inhibition of IL‐6 (87.55% and 82.75%, respectively). These compounds were further explored for anti‐arthritic activity in vivo using the Incomplete Freund's Adjuvant Model and by morphological and histopathological studies of the inflamed paw. Compound 4b was significantly more active than compound 7b and both were found to be slightly less active than methotrexate. These findings indicate that a benzimidazole nucleus linked to a benzene sulphonyl moiety may prove to be a useful template for the development of new chemical moieties against RA.

EMIM] [OAc]: An Efficient Ionic Liquid Medium for the Synthesis of New 4-(furan/pyrrole/thiophene-2-yl)-3, 4-dihydro-1H-chromeno [4,3-d] pyrimidine-2,5-diones and Molecular Docking Studies

Abstract: An efficient synthesis of Chromeno[b]pyrimidine derivatives 4 has been achieved by treating 4-hydroxy-2H-chromen-2-one 1, furan-2-carbaldehyde / 1H-pyrrole-2-carbaldehyde/ thiophene-2- carbaldehyde 2, and urea/thiourea 3 at 65-70 °C for 90-120 min using 1-Ethyl-3-methylimidazolium acetate as ionic liquid and medium with good yields 86-90%. This synthetic method has numerous advantages, including high yields, a simple protocol, environmental friendliness, brief reaction times, and mild reaction conditions. Using a catalytically active ionic liquid as the medium eliminates the need for a catalyst and a solvent. In this study, the docking score of the synthesized compounds was found to be between -8 to -9 kcal/mol similar to the co-crystal. Additionally, the compounds maintained their amino acid interactions with Tyr 281 (coagulation protein; 6WV3) and Thr 179 (tubulin polymerization protein; 5LYJ.pdb).

Screening and identification of phytochemicals from Acorus calamus L. to overcome NDM-1 mediated resistance in Klebsiella pneumoniae using in silico approach

Klebsiella pneumoniae is a potent human pathogen and a prevalent ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species). Considerably, K. pneumoniae becomes a major clinical problem due to numerous AMR genes [extended-spectrum β-lactamase, plasmid-mediated AmpC, carbapenemases, tigecycline resistance, and New Delhi Metallo-β-lactamase-1 (NDM-1)] and can hydrolyse the majority of β-lactam antibiotics. Hence, targeting NDM-1 could be an effective approach to eradicate K. pneumoniae pathogenesis. A plethora of reports suggests that the plant compounds possess an anti-microbial activity and their utilization could be a promising strategy to develop novel antibiotics. Our study utilized the hydromethanolic leaves extract of Acorus calamus L. (AC) to target NDM-1 containing K. pneumonia using an in silico approach. At first, we determined the phytochemical composition of AC using GC-HRMS. Further, the phytoconstituents were screened against the NDM-1 (PDB ID: 3ZR9) of K. pneumoniae through molecular docking studies. Our results revealed the compounds from AC such as [(2R,4S,6R,7S,8R,9S,13S)-16-hydroxy-5’,7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.02,9.04,8.013,18]icos-1(12)-ene-6,2’-oxane]-11-one (-9.5 kcal/mol), 4,4,5,8-tetramethyl-2,3-dihydrochromen-2-ol (-6.6 kcal/mol), 5-chloro-2-(2,4-dichloro phenoxy)phenol (-6.0 kcal/mol), [(3S,3aS,6R,6aS)-3-nitrooxy-2,3,3a,5,6,6a-hexahydrofuro[3,2-b]furan-6-yl] nitrate (-5.7 kcal/mol), 4-(3-hydroxyprop-1-enyl)-2-methoxyphenol (-5.6 kcal/mol), and (E)-3-(2,4-dimethoxyphenyl)prop-2-enoic acid (-5.6 kcal/mol)] possess substantial docking scores against NDM-1. Therefore, our study concludes that phytochemicals of AC may inhibit NDM-1-mediated resistance in K. pneumoniae and could be an alternative therapeutic strategy for targeting NDM-1-containing K. pneumoniae.

Bioassay-guided isolation and in Silico characterization of cytotoxic compounds from Hemimycale sp. Sponge targeting A549 lung cancer cells

Bioassay-guided fractionation approach led to identification of two novel compounds; (4-(hydroxymethyl)-3-methoxy-1H-pyrazol (1) and mycalene (2), alongside with four known metabolites; octadecane (3), hexatriacontane (4), 1-heneicosanol (5) and heptatriacontanoic acid (6) from the Red Sea marine sponge Hemimycale sp. The ethyl acetate fraction showed a noticeable cytotoxic activity against the lung cancer cell line (A549) with IC50 value of 75.54 µg/ mL. Structural elucidation was achieved using a combination of 1D and 2D nuclear magnetic resonance (NMR) spectroscopy and high-resolution electrospray ionization-mass spectrometry (HR-ESI-MS). To elucidate the potential mechanism of action behind the cytotoxic effects against lung cancer, a multi-faceted approach combining in silico network pharmacology, experimental validation, and molecular docking studies were employed. Both compounds, designated as 1 and 2, demonstrated significant binding affinities to predicted target proteins, with docking scores of -4.789 and − 4.421 kcal/mol, respectively. These results lay the groundwork for further investigation into the therapeutic potential of these novel compounds from Hemimycale sp. as promising candidates for lung cancer treatment.

Computational Analysis of Interactions Between Drugs and Human Serum Albumin.

Drug molecules exist as complexed with serum proteins such as human serum albumin (HSA) and/or unbound free form in the blood circulation. Drugs can be effective only when they are free. Thus, it is important to understand aspects that are important for interaction between drugs and interacting proteins. In this study, interactions among 2990 FDA approved drugs and HSA were computational analyzed to unravel principles that are critical for drug-HSA interactions. Docking results showed that drugs have higher affinity toward cavity-1 (C1) than cavity-2 (C2). A total of 1131 drug molecules have docking score greater than 60 while 768 molecules have docking score greater than 60 when they are docked in C2. In addition, three solvent channels have potential to direct solvent to C1 cavity while C2 does not have any effective channel. The post MD analyses demonstrated that drugs are making polar interactions with basic amino acids in the binding cavities. Verbscoside and ceftazidime both have stable low RMSD values throughout MD simulation with 2 Å on average in C1 cavity. The ligand RMSD shows less stability for verbscoside, which is around 4 Å when it is in complex with HSA in C1. The individual contribution of the residues K192, K196, R215, and R254 to ceftazidime are -1.92 ± 0.18, -3.09 ± 0.09, -2.17 ± 0.17, and - 2.32 ± 0.098, respectively. These residues contribute the binding energy of the verbscoside by -6.06 ± 0.08, -2.10 ± 0.06, and - 1.57 ± 0.03 kcal/mol individually in C1 cavity. C2 is making polar interactions with drug via R469, K472, and K488 residues and their contribution to the two drugs are -3.13 ± 0.21 kcal/mol for R469, -1.94 ± 0.18 kcal/mol for K472, and -1.96 ± 0.11 kcal/mol for K488 to total binding energy of ceftazidime. The binding energy of verbscoside is 57.17 ± 7.00 kcal/mol and Arg-407 has the highest contribution this bind energy individually with -4.29 ± 0.12 kcal/mol. Drugs with hydrogen bond donor/acceptor chemical adducts such as verbscoside involve higher hydrogen bond formation in C1 pocket. Ceftazidime makes interaction with HSA toward hydrophobic residues, L384, L404, L487, and L488 in the C2 cavity.

Identification of potential inhibitors for MAP4K4 in glaucoma using Meta-Dynamics-Based dissociation free energy calculation

Glaucoma, a prevalent eye ailment causing irreversible vision loss, affects over 295 million individuals globally, necessitating the exploration of novel therapeutic avenues. Despite extensive research on targets like the phosphodiesterase enzyme and rho kinase, the potential of MAP4K4 in glaucoma remains untapped. This study aims to identify potent MAP4K4 inhibitors to counteract retinal cell apoptosis and oxidative stress associated with glaucoma. Using HTVS and XP docking, 911,059 compounds were screened. The MMGBSA calculation and pharmacokinetics analysis were used to shortlist the compounds. After performing 75 molecular dynamics simulations, further meta-dynamics were employed to calculate dissociation-free energy and find potential MAP4K4 inhibitors. Findings indicated that ZINC06717217 and ZINC38836256 exhibited remarkable promise, with docking scores of −9.57 and −11.12 and MMGBSA binding energies of −91.07 kcal/mol and −87.52 kcal/mol, respectively. Comparative analysis with the reference compound Q27453723 underscored their superior stability, requiring dissociation-free energies of −15.11 kcal/mol and −12.46 kcal/mol to disengage from the docked complex. This underscored their robust binding affinity. ZINC06717217 and ZINC38836256 show promising stability and strong binding to the MAP4K4 protein. Hence, these findings are promising in inhibiting MAP4K4 for glaucoma treatment, potentially leading to more effective treatment and curing blindness. Key messagesFirst to incorporate the dissociation-free energy for identifying compounds for glaucoma treatment.In-silico analysis showed that ZINC06717217 and ZINC38836256 are promising compounds for targeting MAP4K4.

Exploring the Therapeutic Potential of Ginkgo biloba Polyphenols in Targeting Biomarkers of Colorectal Cancer: An In-silico Evaluation.

Colorectal cancer (CRC) is a major contributor to cancer-related deaths worldwide, driving the need for effective anticancer therapies with fewer side effects. The exploration of Ginkgo biloba, a natural source, offers a hopeful avenue for novel treatments targeting key colorectal biomarkers involved in CRC treatment. The aim of this study was to explore the binding affinity of natural molecules derived from G. biloba to essential biomarkers associated with CRC, including Kirsten rat sarcoma virus, neuroblastoma RAS mutations, serine/threonine-protein kinase B-Raf, phosphatidylinositol 3'-kinase, and deleted colorectal cancer, using molecular docking. The focus of this research was to evaluate how effectively these molecules bind to specified targets in order to identify potential inhibitors for the treatment of CRC. A total of 152 polyphenolic compounds from G. biloba were selected and subjected to molecular docking simulations to evaluate their interactions with CRC-related biomarkers. The docking results were analysed to identify ligands exhibiting strong affinities towards the targeted genes, suggesting potential inhibitory effects. Docking simulations unveiled the strong binding affinities between selected polyphenolic compounds derived from G. biloba and genes associated with CRC. The complex glycoside structures that are found in flavonols are of significant importance. These compounds, including derivatives with distinctive arrangements, exhibited promising docking scores, signifying substantial interactions with the targeted biomarkers. The study demonstrates the potential of G. biloba-derived molecules as effective anticancer agents for colorectal cancer. The identified ligands exhibit strong interactions with crucial CRC-related biomarkers, suggesting potential inhibition ability. Further in vitro and in vivo investigations are needed to validate and build upon these promising findings, advancing the development of novel and efficient CRC therapies.

A novel quinazoline derivative exhibits potent anticancer cytotoxicity via apoptosis and inhibition of angiogenesis in DMBA-induced mammary gland carcinoma.

Mammary gland carcinoma is one of the most prevalent and deadly diseases among women globally. It is a type of solid malignant tumor. In this malignant tumor, the microenvironment becomes hypoxic in rapidly proliferating cancer cells. These cells undergo adaptive changes through the expression of hypoxia-inducible factor-1alpha (HIF-1α) which is regulated by factor inhibiting HIF-1α (FIH-1). Considering this, we hypothesized that the chemical activation of FIH-1 would inhibit the hypoxic activity of HIF-1α in mammary gland carcinoma. A library of 67,609 chemical compounds was virtually screened against FIH-1 based on Lipinski's rule from the ZINC database. The BBAP-8 has been selected based on an excellent docking score (-8.352 Kcal/mol), favorable ADMET, and potential FIH-1 activator profile. Further, its in-vitro cytotoxicity and apoptotic activity were scrutinized against MCF-7 cells and in-vivo activity against 7,12-dimethylbenz[a]anthracene (DMBA) induced mammary gland carcinoma in Wistar rats. It exhibited significant cytotoxicity (IC50 = 16.59 ± 0.49 μM) and activated apoptosis when scrutinized through DAPI, AO/EB, and JC-1 staining. Also, oral administration of BBAP-8 restored hemodynamic changes, normalized tissue architecture, and corrected metabolic abnormalities. The western blot analysis and mRNA expression analysis validated that BBAP-8 has the potential to activate FIH-1 with the downregulation of GLUT-1, VEGF, and Twist-1. Moreover, BBAP-8 fostered apoptosis, when evaluated through BCL-2, BAX, Caspase-8, and Caspase-3. Based on research findings, this implies that BBAP-8 activates FIH-1 and can be effective in chemotherapeutic treatment of mammary gland carcinoma.

Extension of impurity profiling on Eltrombopag olamine to in-silico Predictions: An Effort to Exploit correlated forced degradation products and known Drug-Related substances in drug discovery

The recent pandemic has highlighted the impact of diseases on global health and the economy. The rapid discovery of new hit molecules remains a tough challenge. Pharmaceutical impurity profiling can be linked to drug discovery through the identification of new hits from compounds identified during the analytical profiling. The present study demonstrates this linkage through the extension of the impurity (forced degradation) profiling of eltrombopag (ELT) olamine, a thrombopoietin (TPO) receptor agonist. The drug was exposed to standard degradation and the degradation products were primarily resolved and identified by UPLC-ESI-MS. This led to the identification of five forced degradation products (FDP). Thirty-three other known related substances (RS) of ELT, identified in the literature, were also considered. Molecular similarity checks were performed using Tanimoto similarity searches. A set of structurally and topologically similar molecules, including ELT and 15 RS, was established and subjected to in-silico toxicity-, absorption-, distribution-, metabolism-, and elimination (ADME) predictions. The RS, predicted with similar or lower toxicity than ELT and a comparable ADME profile, were subjected to molecular docking to trace changes in TPO receptor affinity. The results indicated that five RS had a high Jaccard’s similarity with ELT and higher or comparable docking scores. These compounds, along with few other impurities were predicted to have lower toxicity, better or comparable absorption, distribution, metabolism, and a better excretion profile than ELT. This justifies their entry as potential novel TPO receptor agonists in drug discovery.

Computational Docking studies of Phenyl Acetic Acid Derivatives with Biological Targets, DNA, Protein and Enzyme

Phenyl acetic acid (PAA) is a well-known biomolecule used in antibiotics and drugs. To elucidate the binding modes of PAA and its derivatives with DNA, Pim kinase protein, and urease enzymes, molecular docking studies were conducted. The results revealed that PAA and its derivatives intercalate with DNA, disrupting its structure and potentially affecting replication, transcription, and repair processes. The 3-chloro-PAA showed the highest docking score (-7.809) and significant polar interactions with DNA residues. For Pim kinase, the compounds exhibited polar interactions with key residues, with 2-propyl PAA demonstrating notable inhibitory effects. Similarly, PAA derivatives interacted effectively with urease enzymes, with the 4-propyl-PAA showing a strong docking score (-8.5250). Overall, the meta-substituted PAAs exhibited superior binding interactions compared to ortho and para-substituted derivatives, suggesting their potential as effective inhibitors for these biological targets.

AlphaFold Meets De Novo Drug Design: Leveraging Structural Protein Information in Multitarget Molecular Generative Models.

Recent advancements in deep learning and generative models have significantly expanded the applications of virtual screening for drug-like compounds. Here, we introduce a multitarget transformer model, PCMol, that leverages the latent protein embeddings derived from AlphaFold2 as a means of conditioning a de novo generative model on different targets. Incorporating rich protein representations allows the model to capture their structural relationships, enabling the chemical space interpolation of active compounds and target-side generalization to new proteins based on embedding similarities. In this work, we benchmark against other existing target-conditioned transformer models to illustrate the validity of using AlphaFold protein representations over raw amino acid sequences. We show that low-dimensional projections of these protein embeddings cluster appropriately based on target families and that model performance declines when these representations are intentionally corrupted. We also show that the PCMol model generates diverse, potentially active molecules for a wide array of proteins, including those with sparse ligand bioactivity data. The generated compounds display higher similarity known active ligands of held-out targets and have comparable molecular docking scores while maintaining novelty. Additionally, we demonstrate the important role of data augmentation in bolstering the performance of generative models in low-data regimes. Software package and AlphaFold protein embeddings are freely available at https://github.com/CDDLeiden/PCMol.

Potential novel HIV-1 reverse transcriptase inhibitors: a modeling and evaluation approach

Human immunodeficiency viru (HIV) is the causative agent of acquired immunodeficiency syndrome (AIDS), a disease that severely weakens the immune system and makes patients more susceptible to infections. Although there is no definitive cure for HIV, advances in drug development offer promising prospects. In this study, we targeted HIV-1 reverse transcriptase by performing virtual screening (VS) to identify novel candidate compounds. From a database of compounds similar to the inhibitor thymidine-5'-triphosphate (TTP), three compounds (CID441663, CID123650073, and CID123789980) were selected for their docking scores, which outperformed those of the reference compound TTP (-6.2302 kcal/mol). These compounds were then subjected to ADMET, PASS, and DFT analyses. Interestingly, all three ligands showed a broad spectrum of predicted antiviral activity, including targets related to human herpes virus and HIV. Specifically, while TTP primarily targets HIV-1 reverse transcriptase, the top three ligands were predicted to target HIV-1 integrase, with CID441663 and CID123789980 displaying higher confidence in this target compared to CID123650073. These findings suggest that the candidate ligands should undergo further in vitro validation to determine their precise roles as inhibitors or antagonists, and to confirm their selective targeting of HIV-related proteins.

Design, Synthesis, and In-Silico Analysis of Thiazole-Embedded Schiff Base Derivatives for Breast Cancer Therapeutic Potential

Thiazole-derived Schiff base compounds possess significant pharmacological properties, influencing various enzymes in metabolic pathways and exhibiting antibacterial, antifungal, anti-inflammatory, antioxidant, and antiproliferative activities. This study delves into the synthesis, characterization, and in-silico analysis of ten thiazole-embedded Schiff base derivatives (TZ1-10), benchmarking them against five Food and Drug Administration (FDA)-approved breast cancer drugs. Molecular docking against multiple therapeutic targets related to fatty acid synthase and cell proliferation (PDB IDs: 4FX3, 4OAR, 3NUP, and 3ERT) alongside ADME and Lipinski rule assessments were conducted. Compounds TZ6 and TZ8 emerged as promising candidates with docking scores of -8.0 kcal/mol and -8.2 kcal/mol respectively against the 4FX3 protein. These findings contribute to a deeper understanding of thiazole-embedded Schiff base derivatives, showcasing their potential for future medicinal and scientific applications.

Repurposed pharmacotherapy: targeting cathepsin L with repurposed drugs in virtual screening.

Proteolytic enzymes are closely associated with cancer and are important in different phases, including tumor growth, angiogenesis, and metastasis. Despite efforts to target matrix metalloproteases (MMPs), clinical trials have often resulted in various side effects such as musculoskeletal pain, joint stiffness, and tendinitis, making them less optimal for chronic cancer treatment. Thus, there is a need for the identification of other protease targets that would provide different approaches towards the management of cancer. Of these targets, Cathepsin L (CatL) is a lysosomal cysteine protease that has been identified as a therapeutic target that is implicated in cancer development and metastasis. In this study, we performed an integrated approach of virtual screening and molecular dynamics (MD) simulations to identify the potential inhibitors of CatL from a library of drugs that have been used for different treatments. Towards this goal, we performed virtual screening of the DrugBank database and found two repurposed drugs, Irinotecan and Nilotinib, against CatL based on their docking profiles, favorable docking scores, and specific interaction with the CatL binding pocket. MD simulations of the Irinotecan and Nilotinib bound structures with CatL were carried out, and the analysis showed that both these compounds could function as CatL inhibitors as the protein-ligand interactions were stable for 300 ns. This study highlights the robustness of these drugs bound to CatL and indicates that they could be repurposed for the treatment of cancer. These findings endorse the use of computer-based approaches for the identification of new inhibitors, and the present study will be a useful resource for future experimental research towards the targeting of CatL in cancer therapeutics.

Unveiling the antibacterial potential of latex-derived phytocomponents from Calotropis gigantea targeting bacterial Penicillin-binding proteins: chemical profiling, in silico docking, and in vitro lab validation

Uncontrolled use of currently accessible medicines has caused antibiotic resistance in bacteria worldwide. This work aimed to undertake molecular docking and chemical profiling of bioactive components extracted from Calotropis gigantea latex, with wet lab confirmation to follow. Gas chromatography was used to analyze the phytochemical profile. The docking tool, Cb-dock2, was used for in-silico analysis. G+ and G- bacterial strains were utilized to confirm the wet lab results. Chemical profiling revealed 18 peaks, and some major bioactive compounds were like phytol, 4-methyl-2- phenylindole and α-tocospiro A. Docking analysis revealed strong interaction against bacterial Penicillin-binding Protein (PBP1a) with docking scores ranging from -5.2 to -7.9 (Vina score). The PBP-Ligand complex has Van der Waals, hydrogen bond, pi-cation, and alkyl bonding interactions, according to the results of the interaction investigations. Calotropis latex successfully suppressed the development of bacterial strains (G+ and G-) with inhibition zones ranging from 1.1 cm to 2.2 cm, as demonstrated by in-vitro tests, indicating their potential as antibacterial medications. The study found that latex-based bioactive compounds have the potential to be used in the pharmaceutical and biotechnology sectors by facilitating the creation of structural alterations that lead to stronger medications. Therefore, this latex-derived compound may open a new pipeline into the development of multi-target antibiotics against a broad-spectrum multidrug-resistant G- bacterium.