Integrative analysis discovers Imidurea as dual multitargeted inhibitor of CD69, CD40, SHP2, lysozyme, GATA3, cCBL, and S-cysteinase from SARS-CoV-2 and M. tuberculosis

Evaluating the polypharmacological potency of indenopyrazole against lung cancer oxidoreductase, chaperone, transferase, and hydrolase proteins

Lung cancer, the deadliest malignancy worldwide, causes 2.2 million cases and 1.8 million deaths annually, accounting for 18% of cancer deaths. Limited early detection, unaffordable treatments, and drug resistance lead to low survival rates, highlighting the urgent need for developing effective, resistance-proof therapies. In this study, we docked the DrugBank library against Lung Cancer Oxidoreductase, Chaperone, Transferase, and Hydrolase Proteins to identify a multitargeted drug candidate, resulting in identifying a promising drug candidate named Indenopyrazole with docking and MM\GBSA scores ranging from -7.337 to -11.62 and -17.82 to -60.38 kcal/mol, respectively. We also evaluated the interaction pattern of the drug candidate with Molecular Interaction Fingerprints and found that the most interacting residues with its counts are 4TRP, 3ASP, 3GLN, 3GLU, 3LYS, 3PHE, and 3TYR. The pharmacokinetics and comparison with standard values supported the candidate, followed by the density functional theory computations. The study was also validated for the WaterMap for water thermodynamics, and its role in binding pockets has also supported the idea that Indenopyrazole has a multitargeted potency. Further, we extended our studies with 100ns MD Simulation in water to analyse the deviations, fluctuations, and intermolecular interactions, and all the 1000 trajectories were evaluated for total complex energy and binding free energy with MM\GBSA concluding wonderful promising results in support of Indenopyrazole as a multitargeted drug candidate-however, its efficacy needs to be experimentally validated.

Isoetin from Isoetaceae Exhibits Superior Pentatransferase Inhibition in Breast Cancer: Comparative Computational Profiling with FDA-Approved Tucatinib

Background: Breast cancer, the most prevalent cancer among women globally, develops primarily in the breast's ducts or lobules. Drug resistance is a significant challenge in treating advanced cases, contributing to over 685,000 breast cancer-related deaths annually, and identifying novel compounds that inhibit key proteins is crucial for developing effective therapies. Methods: In this study, five transferase proteins with PDB IDs were selected due to their involvement in breast cancer: 1A52, 3PP0, 4EJN, 4I23, and 7R9V. Multitargeted docking studies were conducted using three different docking strategies and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) to calculate the binding affinities against the ZINC Natural compound library. Isoetin (ZINC000006523948), found mainly in Isoetaceae, was identified, and the results were compared with the Food and Drug Administration (FDA)-approved drug Tucatinib. In addition, molecular interaction fingerprints and pharmacokinetic profiling were evaluated. We also performed 5 ns WaterMap simulations to identify hydration sites and interactions, followed by 100 ns molecular dynamics (MD) simulations and MM/GBSA to assess the stability of the Isoetin-protein complexes. Results: The docking results indicated that Isoetin demonstrated superior binding and docking scores ranging from -9.901 to -13.903 kcal/mol compared to Tucatinib, which showed values between -4.875 and -10.948 kcal/mol, suggesting Isoetin's potential efficacy as a therapeutic agent for breast cancer. Interaction fingerprints revealed significant interactions between Isoetin and key residues, including 28LEU, 12MET, 9PHE, 7ASP, 6ASN, and 6THR. The pharmacokinetics and DFT analysis of Isoetin supported its potential as a viable drug candidate. Furthermore, the 5 ns WaterMap simulations identified various hydration sites, and the 100 ns MD simulations showed that the Isoetin-protein complexes exhibited minimal deviations and fluctuations, indicating better stability than Tucatinib, and MM/GBSA confirmed Isoetin's superior binding stability. Conclusions: Isoetin, a natural compound identified through in silico screening, demonstrates significant promise as a potential therapeutic agent for breast cancer as it outperforms the FDA-approved drug Tucatinib, the respective native and FDA-approved drug. However, experimental validation is necessary before considering Isoetin for clinical use.

Anticancer potential of novel benzothiazolyl piperidine-3-carboxamide derivatives as CDKs and VEGFR2 multi-target kinase inhibitors

The inhibition of cyclin-dependent kinases is a viable anticancer therapy due to their critical function in regulating cell cycle progression and transcription. The present study intended to design novel benzothiazolyl piperidine-3-carboxamide derivatives as multi-target CDKs and VEGFR2 inhibitor. Novel benzothiazolyl piperidine-3-carboxamide derivatives varying smaller and bulkier N-substitution at piperidine motif (4a-f) were designed based on the key structural features of SNS-032 (a CDK and VEGFR2 inhibitor). The compounds were subjected to extra-precision docking on seven CDKs and VEGFR2 kinase targets. The results revealed superior score/interaction of compounds with three CDKs (CDK2, CDK5, and CDK6) and VEGFR2, as compared to SNS-032. The best poses of 3, 4b, 4c and SNS-032 were used in WaterMap study to analyze the hydration sites. MD simulations (100 ns) in the TIP3P water model for 4c and SNS-032 were performed to analyze the trajectories for the deviation, fluctuations and intermolecular interaction, followed by the binding free energy calculations (MM-GBSA). All the compounds were synthesized and spectroscopically characterized by NMR, HPLC and LC-MS. In vitro CDKs (CDK2, CDK5, and CDK6) and VEGFR2 kinase inhibition assays revealed higher potency of compounds 3 (IC50 0.026 µM) and 4c (IC50 0.048 µM) as compared to SNS-032 (IC50 0.052 µM) against CDK2, compounds 3 (IC50 0.315 µM), 4a (IC50 0.248 µM), 4b (IC50 0.276 µM), and 4c (IC50 0.338 µM) as compared to SNS-032 (IC50 0.476 µM) against CDK5, compounds 3 (IC50 0.221 µM), 4a (IC50 0.256 µM), 4b (IC50 0.282 µM), 4c (IC50 0.236 µM), and 4e (IC50 0.274 µM) as compared to SNS-032 (IC50 0.365 µM) against CDK6, and comparable potency of compound 4b (IC50 0.136 µM) with Sorafenib (IC50 0.114 µM) against VEGFR2. Furthermore, anticancer screening of compounds (3 and 4a-f) was performed against NCI (USA) 60 cancer cell lines by sulforhodamine B (SRB) colorimetric assay that revealed good to excellent anticancer activity.

Alternative use of droxidopa for treating cervical cancer: inhibiting transferase, cell cycle signalling, and transport proteins via multitarget docking, DFT, MD simulations, and binding free energy studies

Cervical cancer develops due to the uncontrolled growth of abnormal cells in the cervix, mainly triggered by a persistent infection with high-risk types of human papillomavirus (HPV), a sexually transmitted virus. Factors that increase the risk include having multiple sexual partners, engaging in sexual activity at an early age, smoking, and a compromised immune system. Globally, it ranks as the fourth most prevalent cancer among women, with over 600000 new cases and 340000 deaths each year. The disease disproportionately impacts women in low- and middle-income countries, where access to screening and vaccination is often limited. Drug resistance emerges when cancer cells evade treatment through genetic mutations, altered targets, and efflux pump overexpression. Multitargeted docking identifies compounds interacting with multiple targets where a drug can inhibit crucial pathways, improving efficacy and reducing resistance chances. In this study, we examined Transferase, Cell Cycle Signalling, and Transport Proteins associated with PDB IDs 2WVI, 2B9R, 3VHX, and 3KND. These targets were subjected to multitargeted docking using an FDA-approved drug library. Droxidopa was identified as a multitargeted drug, with docking scores ranging from - 5.99 to - 11.37 kcal/mol and MM/GBSA scores between - 20.13 and - 43.00 kcal/mol. The interaction fingerprints identified the most interacted residues with counts are 4GLN, 4GLU, 3ARG, and 3TRP, and the Pharmacokinetics and DFT analysis favoured the compound's suitability. Furthermore, 5 ns (nanoseconds) WaterMap for hydration sites and 100 ns MD simulation in NPT ensemble at 330 K temperature have resulted in acceptable deviations, fluctuations, and many intermolecular interactions, and binding free energy computations have favoured droxidopa's use against cervical cancer-however, experimental studies are needed before its use including the in-vitro and in-vivo studies.

Targeting Plasmodium falciparum Schizont Egress Antigen-1 in Infected Red Blood Cells: Docking-Based Fingerprinting, Density Functional Theory, Molecular Dynamics Simulations, and Binding Free Energy Analysis

Background: Malaria remains a global health crisis, with the World Health Organization (WHO) reporting 241 million cases and 627,000 deaths worldwide in 2020, predominantly affecting Sub-Saharan Africa. The region accounted for 95% of cases and 96% of deaths, reflecting the immense challenges in malaria prevention and treatment. Plasmodium falciparum Schizont Egress Antigen-1 (PfSEA-1) is crucial in facilitating immune evasion and promoting the sequestration of infected red blood cells (RBCs), contributing to severe malaria symptoms, including cerebral malaria, and necessitates the urgent identification of novel or repurposed drugs targeting PfSEA1. Methods: The protein structure of PfSEA-1 (UniProt ID: A0A143ZXM2) was modelled in three dimensions, prepared, and subjected to a 50 ns molecular dynamics (MD) simulation to achieve a stable structure. The equilibrated structure was minimised for molecular docking against the DrugBank compound library. Docking analysis identified potential inhibitors, including Alparabinos, Dihycid, Ambenzyne, Amiflupipquamine, Ametchomine, and Chlobenethyzenol, with docking scores ranging from -8.107 to -4.481 kcal/mol. Advanced analyses such as interaction fingerprints, density functional theory (DFT), and pharmacokinetics evaluations were conducted. Finally, a 100 ns MD simulation in the NPT ensemble was performed to assess the stability of protein-ligand complexes, with binding free energy and total energy calculations derived from the simulation trajectories. Results and Discussion: The identified compounds exhibited satisfactory pharmacokinetic profiles and binding interactions with PfSEA-1. The MD simulations demonstrated overall stability, with minor fluctuations in some instances. Key intermolecular interactions were observed, supporting the binding stability of the identified compounds. Binding free energy calculations confirmed favourable interactions, underscoring their potential as therapeutic agents against Plasmodium falciparum. While the in silico results are promising, experimental validation is essential to confirm their efficacy and safety for clinical use. Conclusion: These findings highlight PfSEA-1 as a promising antimalarial target and identify potential inhibitors with strong binding affinities and favourable pharmacokinetics. While the computational results are encouraging, further in vitro and in vivo validation is necessary to confirm their therapeutic potential and facilitate future drug development.

Investigating the Inhibitory Effects of Paliperidone on RAGEs: Docking, DFT, MD Simulations, MMPBSA, MTT, Apoptosis, and Immunoblotting Studies

Chronic diseases such as diabetes and cancer are the leading causes of mortality worldwide. Receptors for Advanced Glycation End products (RAGEs) are ubiquitous factors that catalyse Advanced Glycation End products (AGEs), proteins, and lipids that become glycated from sugar ingestion. RAGEs are cell surface receptor proteins and play a broad role in mediating the effects of AGEs on cells, contributing to modifying biological macromolecules like proteins and lipids, which can cause Reactive Oxygen Species (ROS) generation, inflammation, and cancer. We targeted RAGE inhibition analysis and screening of United States Food and Drug Administration (FDA) libraries through molecular docking studies that identified the four most suitable FDA compounds: Zytiga, Paliperidone, Targretin, and Irinotecan. We compared them with the control substrate, Carboxymethyllysine, which showed good binding interaction through hydrogen bonding, hydrophobic interactions, and π-stacking at active site residues of the target protein. Following a 100 ns simulation run, the docked complex revealed that the Root Mean Square Deviation (RMSD) values of two drugs, Irinotecan (1.3 ± 0.2 nm) and Paliperidone (1.2 ± 0.3 nm), were relatively stable. Subsequently, the Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) determined that the Paliperidone molecule had a high negative energy of -13.49 kcal/mol, and the Absorption, Distribution, Metabolism, and Excretion (ADME) properties were in control for use in the mentioned cases. We extended this with many in vitro studies, including an immunoblotting assay, which revealed that RAGEs with High Mobility Group Box 1 (HMGB1) showed higher expression, while RAGEs with Paliperidone showed lower expressions. Furthermore, cell proliferation assay and Apoptosis assay (Annexin-V/PI staining) results revealed that Paliperidone was an effective anti-glycation and anti-apoptotic drug-however, more extensive in vivo studies are needed before its use.

Lucidin from Rubia cordifolia Outperforms FDA-Approved Lapatinib as a Potential Multitargeted Candidate for Breast Cancer Signalling Proteins

Background: Breast cancer remains a significant global health concern, with approximately 2.3 million diagnosed cases and 670,000 deaths annually. Current targeted therapies face challenges such as resistance and adverse side effects. This study aimed to explore natural compounds as potential multitargeted breast cancer therapeutics, focusing on Lucidin, an anthraquinone derived from Rubia cordifolia, and comparing its efficacy with Lapatinib, an FDA-approved drug. Methods: We performed multitargeted molecular docking studies on key breast cancer proteins using a natural compound library from ZINC. Comparative analyses of Lucidin and Lapatinib included molecular interaction fingerprints, pharmacokinetics, WaterMap computations (5 ns) to assess water thermodynamics and binding interactions, and Molecular Dynamics Simulations (100 ns) in water to evaluate complex stability and dynamic behaviour. Results: Lucidin demonstrated significant binding affinity and interaction potential with multiple breast cancer targets, outperforming Lapatinib in stability and binding interactions. WaterMap analysis revealed favourable hydration site energetics for Lucidin, enhancing its efficacy. The multitargeted profile of Lucidin suggests a broader therapeutic approach with potential to overcome resistance and side effects associated with Lapatinib. Conclusions: Lucidin shows promise as a novel, multitargeted anti-breast cancer agent with improved efficacy over Lapatinib. These findings provide a foundation for further in vitro and in vivo validation to develop Lucidin as a potential therapeutic option for breast cancer treatment.

Molecular Regulator Driving Endometriosis Towards Endometrial Cancer: A Multi-Scale Computational Investigation to Repurpose Anti-Cancer drugs

Endometriosis is a gynecological disorder among reproductive-aged women. Recent epidemiological investigations suggest endometriosis increases the risk of endometrial cancer. However, the molecular entity leading to endometriosis-to-endometrial cancer is largely unknown. This study aimed to combine a variety of computational approaches to identify the key therapeutic target promoting endometriosis-to-endometrial cancer and screen potential inhibitors against target to prevent cancer development. Our systematic investigations, includes transcriptomic profiling, protein network, pharmacophore modeling, docking, binding free energy calculation, dynamics simulation, and quantum mechanics. The gene expression analysis on endometriosis and endometrial cancer was performed and showed 108 shared upregulated genes in both conditions. Further construction of interaction network with 108 genes showed intercellular adhesion molecule 1 (ICAM1) to be a crucial molecule with a high degree of connectivity that influences vital mechanisms related to cancer pathways. We then generated ligand-based pharmacophore models using established ICAM1 inhibitors. Among the models, the ADRRR_8 pharmacophore exhibited a robust area under curve (AUC = 0.83), was employed to screen 1739 anti-cancer drugs. On screening, 421 anti-cancer drugs displayed ICAM1-inhibiting pharmacophore features. Further, the docking of 421 drugs with ICAM1 showed lanreotide (-7.80 kcal/mol) with better affinity than the reference ICAM1 inhibitor (-3.59 kcal/mol). Further validation though binding free energy and dynamics simulation of the lanreotide-ICAM1 complex showed a high binding affinity of -55.90 kcal/mol and contributed stable confirmation. According to quantum chemical calculations, lanreotide's electronic properties favour ICAM1 binding with highest occupied molecular orbital was -6.91 eV and lowest unoccupied molecular orbital was -3.93 eV. Our study supports using lanreotide to treat endometriosis, which could delay or prevent endometrial cancer. These predictions need to be confirmed and examined to determine the use of lanreotide in endometriosis treatment.

Unveiling the potency of FDA-approved oxidopamine HBr for cervical cancer regulation and replication proteins

Cervical Cancer remains a women's health concern worldwide and ranks among the most prevalent cancers, particularly in developing countries. Many women are diagnosed with cervical cancer, with a substantial number succumbing to the disease even after the availability of vaccines and drugs. The tumour microenvironment often exhibits immune evasion, including suppression of T-cell activity and altered cytokine, impacting the efficacy of therapeutic interventions and highlighting the need for treatments to modulate the immune response. Despite efforts to promote HPV vaccination and regular screenings, it causes many deaths, underscoring the urgent need for continued research, healthcare access, and rapid drug development or repurposing. In this study, we identified various proteins involved in cervical cancer cell cycle regulation and DNA replication proteins, performed the multitargeted docking with an FDA-approved library, and identified Oxidopamine HBr as a multitargeted drug. Studies extended with pharmacokinetics and compared with the standard values followed by DFT, which supported the compound as a multitargeted inhibitor. Further, the docked complexes were taken for the interaction fingerprints, and it was identified that there are many 9 polar, 5 hydrophobic, 2 aromatic, and 2 basic residues. We extended our studies for 100ns MD Simulation in water, and the computations explored the deviation and fluctuations under 2Å and many intermolecular interactions; the same trajectory files were used for the MM\GBSA studies. All the studies have supported the Oxidopamine HBr as a cervical cancer multitargeted inhibitor-however, experimental studies are needed before human use.