Pharmacoinformatics approach for the identification of Polo-like kinase-1 inhibitors from natural sources as anti-cancer agents

Copper(II)-photocatalyzed Hydrocarboxylation of Schiff bases with CO2: antimicrobial evaluation and in silico studies of Schiff bases and unnatural α-amino acids

We synthesized and characterized two copper(II) complexes: [CuL2Cl]Cl and [CuL'2Cl]Cl, where L = 2,2'-bipyridine and L' = 4,4'-dimethyl-2,2'-bipyridine. We evaluated their photocatalytic hydrocarboxylation properties on a series of synthesized Schiff bases (SBs): (E)-1-(4-((5-bromo-2-hydroxybenzylidene)amino)phenyl)ethanone (SB1), (E)-N-(4-(dimethylamino)benzylidene)benzo[d]thiazol-2-amine (SB2), (E)-4-Bromo-2-((thiazol-2-ylimino)methyl)phenol (SB3), and (E)-4-((5-bromo-2-hydroxybenzylidene)amino)-1,5-dimethyl-2-phenyl-1H-pyrazol-3(2H)-one (SB4). Under mild photocatalytic reaction conditions (room temperature, 1 atm CO2, 30-watt Blue LED light), the derivatives of α-amino acids UAA1-4 were obtained with yields ranging from 5% to 44%. Experimental results demonstrated that [CuL2Cl]Cl exhibited superior photocatalytic efficiency compared to [CuL'2Cl]Cl, attributed to favourable electronic properties. In silico studies revealed strong binding strengths with E. faecalis DHFR (4M7U) for docked Schiff bases (SB) and unnatural α-amino acids (UAAs). In vitro studies further demonstrated significant antimicrobial and antifungal activity for SB2, SB3, and SB4, while none of the synthesized UAAs exhibited such properties, primarily due to the electronic and binding properties of these molecules.

Designing a novel drug-drug conjugate as a prodrug for breast cancer therapy: in silico insights

Breast cancer (BC) poses a significant global health threat, necessitating innovative therapeutic approaches. The ribosomal s6 kinase 2 (RSK2) has emerged as a promising target due to its roles in cell proliferation and survival. This study proposes a drug-drug conjugate prodrug comprising Methotrexate (hydrophobic) and Capecitabine (hydrophilic) for BC treatment. In silico approaches, including Molecular Docking, Molecular Dynamics Simulations, MM-PBSA, ADME, and DFT calculations were employed to evaluate the prodrug's potential. The designed MET-CAP ligand exhibits a robust docking score (-8.980 kcal/mol), superior binding affinity (-53.16 kcal/mol), and stable dynamic behavior (0.62 nm) compared to native ligands. The DFT results reveal intramolecular charge transfer in MET-CAP (HLG = 0.09 eV), indicating its potential as a BC inhibitor. ADME analysis suggests satisfactory pharmaceutically relevant properties. The results indicate that the conjugated MET-CAP ligand exhibits favorable binding characteristics, stability, and pharmaceutically relevant properties, making it a potential RSK2 inhibitor for BC therapy. The multifaceted approach provides insights into binding interactions, stability, and pharmacokinetic properties, laying the foundation for further experimental validation and potential clinical development.

Multispectroscopic and computational insights into amyloid fibril formation of alpha lactalbumin induced by sodium hexametaphosphate

The impact of sodium hexametaphosphate (SHMP) on the aggregation behavior of α-lactalbumin (α-LA) was studied at pH 7.4 and 2.0. Turbidity measurements showed a concentration-dependent aggregation of α-LA at pH 2.0 in the presence of SHMP, while no aggregation was observed at pH 7.4. Light scattering (LS) and Thioflavin-T (ThT) data revealed that the aggregation was rapid, following nucleation-independent pathways. In other kinetics experiments such as turbidity and ThT confirmed that SHMP-induced α-LA aggregation was dependent on SHMP concentration rather than incubation time. Once formed, the aggregates remained unchanged for up to five days. Intrinsic fluorescence studies indicated conformational changes in α-LA upon SHMP addition, and dye-binding assays with ThT and Congo Red demonstrated the formation of amyloid-like aggregates. Far-UV circular dichroism (CD) data suggested a structural transition from α-helical to β-structures in α-LA in the presence of SHMP at pH 2.0. Molecular docking studies confirmed stronger interactions between α-LA and SHMP at pH 2.0 (ΔG = -6.2 kcal/mol) compared to pH 7.4 (ΔG = -5.3 kcal/mol), driven by electrostatic forces and hydrogen bonding. These results suggest that SHMP induces amyloid-like aggregation of α-LA, particularly at acidic pH.

Synergistic anti-tumorigenic effect of diosmetin in combination with 5-fluorouracil on human colon cancer xenografts in nude mice

5-Fluorouracil (5-FU) is frequently used to treat colorectal cancer (CRC), but its clinical application is limited by its toxicity. Natural compounds have been combined with chemotherapeutic drugs to reduce chemotherapy-related toxicity. Diosmetin, a natural flavonoid, has demonstrated anticancer effects against CRC. This study investigated diosmetin's potential in combination with 5-FU using a murine model of HCT-116 colon cancer xenografts in nu/nu nude mice. HCT-116 cells were injected into the right flanks of mice, and once tumors reached a size of 50 mm3, the mice were treated with diosmetin (100 mg/kg), 5-FU (30 mg/kg), or a combination of both at two dose levels (100 + 30 mg/kg and 50 + 15 mg/kg) for 4 weeks. Blood and tumors were collected on the final day for further analysis. Mice treated with the higher combination dose exhibited the smallest tumor volume (330.91 ± 88.49 mm3). Biochemistry and histology analysis showed no toxicity or abnormalities in the liver, kidney, and heart with the combination therapy. Immunohistochemistry results revealed a notable reduction in the proliferation marker (Ki67) and inflammation marker (TLR4) in tumors from high-dose combination-treated mice. Moreover, immunofluorescence data indicated increased levels of apoptotic markers (Bax, Caspase-3, p53, p21) and downregulation of anti-apoptotic protein (Bcl-2) in the high-dose combination group. The findings suggest that 100 mg/kg of diosmetin combined with 30 mg/kg 5-FU significantly reduced tumor volume and had a less toxic effect on the heart compared to 5-FU monotherapy.

Exploring Moroccan Medicinal Plants for Anticancer Therapy Development Through In Silico Studies

BACKGROUND

Angiogenesis is a crucial process in the growth and proliferation of cancer, enabling tumor growth through the formation of new vasculature and the supply of nutrients and oxygen to growing malignant cells. This disease-promoting process can be targeted through the inhibition of tyrosine kinase enzymes.

OBJECTIVES

The objective of this study is to evaluate the anticancer potential of various Moroccan plants from different regions. While these plants have a rich history of traditional medicinal use, they have not been extensively investigated as anticancer therapies.

METHODS

This study employed a multifaceted approach to evaluate the anticancer potential of various Moroccan plants. Receptor-ligand docking and virtual screening were used to assess the binding affinity of phytocompounds to the EGFR and VEGFR2 receptors. Additionally, predictive pharmacokinetic analyses were conducted to evaluate the ADMET properties of the selected compounds, followed by molecular dynamics simulations to analyze the stability of the receptor-ligand complexes.

RESULTS

In our research, we identified three notable active compounds-catechin, 4-O-glucoside ferulic acid, and 3-glucoside resveratrol-in the Moroccan plant Ajuga iva L. These findings suggest that Ajuga iva L. may possess significant potential for cancer inhibition.

CONCLUSIONS

This research highlights the potential of the Moroccan plant Ajuga iva L. as a source of active compounds with significant anticancer properties. Further investigation is essential to validate these findings and explore new therapeutic avenues based on these traditional resources.

Binding of a Drug (Colchicine) to L-Asparaginase Enzyme Using Multispectroscopic, Thermodynamics, and Simulation Studies: Possible Implication in Acute Lymphoblastic Leukemia Treatment

The research aims to elucidate how drug interactions affect the activity of L-asparaginase (L-ASNase), an essential enzyme in cancer treatment, especially for acute lymphoblastic leukemia (ALL). Understanding these interactions is crucial for optimizing treatment effectiveness and reducing adverse effects. This study explores the intricate molecular interactions and structural dynamics of L-ASNase upon binding with colchicine. Fluorescence quenching experiments were conducted at various temperatures (298, 303, and 310 K), revealing notable interactions between L-ASNase and colchicine. These interactions were characterized by a reduction in fluorescence intensity and a blue shift in emission maxima. Additional analyses, including the determination of Stern-Volmer quenching constants (KSV), bimolecular quenching rate constants (kq), and thermodynamic parameters, indicated a static quenching mechanism with moderate binding affinities (Ka: 1.40-2.71 × 104 M-1) across different temperatures. Thermodynamic study suggested positive enthalpy and entropy changes (ΔH° = -10.26 kcal mol-1; ΔS° = -14.19 cal mol-1 K-1), suggesting a spontaneous reaction with negative ΔG° values (-5.86 to -6.03 kcal mol-1). FRET measurements supported optimal distances (r and Ro) for FRET occurrence, reinforcing the static quenching mechanism. Molecular docking further supported these findings, revealing a 1:1 stoichiometric binding ratio for L-ASNase:colchicine and elucidating specific binding orientations and interactions critical for complex stability. Subsequent molecular dynamics simulations spanning 100 ns underscored the stability of the L-ASNase-colchicine complex, with minimal deviations observed in key structural parameters such as RMSD, RMSF, Rg, and SASA. Additionally, spectroscopic analyses, including circular dichroism (CD), synchronous fluorescence, and 3D fluorescence provided insights into the conformational changes and alterations in the microenvironment of aromatic amino acid residues in L-ASNase upon colchicine binding. Moreover, L-ASNase activity was slightly reduced by 25% in the presence of colchicine. This comprehensive investigation sheds light on the molecular intricacies of the L-ASNase-colchicine complex, advancing our understanding of drug-target interactions and offering potential avenues for therapeutic applications.

Design, Synthesis, and Bioevaluation of Novel NLRP3 Inhibitor with IBD Immunotherapy from the Virtual Screen

NLRP3, a crucial member of the NLRP family, plays a pivotal role in immune regulation and inflammatory modulation. Here, we report a potent and specific NLRP3 inhibitor Z48 obtained though docking-based virtual screening and structure-activity relationship studies with an IC50 of 0.26 μM in THP-1 cells and 0.21 μM in mouse bone marrow-derived macrophages. Mechanistic studies indicated that Z48 could bind directly to the NLRP3 protein (KD = 1.05 μM), effectively blocking the assembly and activation of the NLRP3 inflammasome, consequently manifesting anti-inflammatory properties. Crucially, with acceptable mouse pharmacokinetic profiles, Z48 demonstrated notable therapeutic efficacy in a mouse model of DSS-induced ulcerative colitis, while displaying no significant therapeutic impact on NLRP3KO mice. In conclusion, this study provided a promising NLRP3 inflammasome inhibitor with novel molecular scaffold, poised for further development as a therapeutic candidate in the treatment of inflammatory bowel disease.

Discovery and prospects of new heterocyclic Isatin-hydrazide derivative with a novel role as estrogen receptor α degrader in breast cancer cells

Introduction: Isatin, a heterocycle scaffold, is the backbone of many anticancer drugs and has previously been reported to engage multiple cellular targets and mechanisms, including angiogenesis, cell cycle, checkpoint pathways and multiple kinases. Here, we report that a novel isatin derivative, 5i, degrades estrogen receptor alpha (ERα) in estrogen-dependent breast cancer cells. This effect of the isatin nucleus has not been previously reported. Tamoxifen and fulvestrant represent standard therapy options in estrogen-mediated disease but have their own limitations. Isatin-based triple angiokinase inhibitor BIBF1120 (Nintedanib) and multikinase inhibitor Sunitinib (Sutent) have been approved by the FDA. Methods: Keeping this in view, we synthesized a series of N'-(1-benzyl-2-oxo-1, 2-dihydro-3H-indol-3-ylidene) hydrazide derivatives and evaluated them in vitro for antiproliferative activities in MCF-7 (ER+) cell line. We further investigated the effect of the most potent compound (5i) on the Erα through Western Blot Analysis. We used in silico pharmacokinetics prediction tools, particularly pkCSM tool, to assess the activity profiles of the compounds. Results and discussion: Compound 5i showed the best antiproliferative activity (IC50 value; 9.29 ± 0.97 µM) in these cells. Furthermore, 5i downregulated ERα protein levels in a dose-dependent manner in MCF-7. A multifaceted analysis of physicochemical properties through Data Warrior software revealed some prominent drug-like features of the synthesized compounds. The docking studies predicted the binding of ligands (compounds) with the target protein (ERα). Finally, molecular dynamics (MD) simulations indicated stable behavior of the protein-ligand complex between ERα and its ligand 5i. Overall, these results suggest that the new isatin derivative 5i holds promise as a new ERα degrader.

Integrated spectroscopic and computational analyses unravel the molecular interaction of pesticide azinphos-methyl with bovine beta-lactoglobulin

Organophosphorus are typically hazardous chemicals used in the pharmaceutical, agricultural, and other industries. They pose a serious risk to human life and can be fatal upon direct exposure. Hence, studying the interaction between such compounds with proteins is crucial for environmental, health, and food safety. In this study, we investigated the interaction mechanism between azinphos-methyl (AZM) and β-lactoglobulin (BLG) at pH 7.4 using a combination of biophysical techniques. Intrinsic fluorescence investigations revealed that BLG fluorescence was quenched in the presence of increasing AZM concentrations. The quenching mechanism was identified as static, as evidenced by a decrease in the fluorescence quenching constant (1.25 × 104, 1.18 × 104, and 0.86 × 104 M-1) with an increase in temperatures. Thermodynamic calculations (ΔH > 0; ΔS > 0) affirmed the formation of a complex between AZM and BLG through hydrophobic interactions. The BLG's secondary structure was found to be increased due to AZM interaction. Ultraviolet -visible spectroscopy data showed alterations in BLG conformation in the presence of AZM. Molecular docking highlighted the significant role of hydrophobic interactions involving residues such as Val43, Ile56, Ile71, Val92, Phe105, and Met107 in the binding between BLG and AZM. A docking energy of -6.9 kcal mol-1, and binding affinity of 1.15 × 105 M-1 suggest spontaneous interaction between AZM and BLG with moderate to high affinity. These findings underscore the potential health risks associated with the entry of AZM into the food chain, emphasizing the need for further consideration of its impact on human health.

Computational investigation of the impact of potential AT2R polymorphism on small molecule binding

For more than a century, the renin-angiotensin system (RAS) has been acknowledged for playing a crucial part in the physiological control of arterial pressure, as well as sodium and fluid balance. It is now generally acknowledged that one of the receptor of RAS system i.e. angiotensin type 2 receptor (AT2R) functions as a repair system during pathophysiologic circumstances and performs a significant protective role. Efforts have been made previously to design suitable agonist and antagonist molecules to potentially modulate AT2R. One of the agonists and antagonists, named C21 and EMA401, has been studied in a number of pathological conditions. Additionally, a wide panel of single nucleotide polymorphisms (SNPs) has been reported for AT2R, which might potentially affect the efficacy of these molecules. Therefore, computational investigations have been carried out to analyze all the SNPs (1151) reported in NCBI to find potential SNPs affecting the active site of AT2R, as this domain is still unexplored. Structures of these polymorphic forms were modeled, and in silico drug interaction studies with C21 and EMA401 were carried out. The two mutants (rs868939201 and rs1042852794) that significantly affect the binding affinity as that of the wild type were subjected to molecular dynamics simulations. Our analysis of native and mutant AT2R and their complexes with C21 and EMA401 indicated that the occurrence of these mutations affects the conformation of the protein and has affected the binding of these ligand molecules. The study's findings will aid in the development of better, more versatile medications in the near future, and also in vitro and in vivo studies might be planned in accordance with recent findings.Communicated by Ramaswamy H. Sarma.

Identification of PLK1-PBD Inhibitors from the Library of Marine Natural Products: 3D QSAR Pharmacophore, ADMET, Scaffold Hopping, Molecular Docking, and Molecular Dynamics Study

PLK1 is found to be highly expressed in various types of cancers, but the development of inhibitors for it has been slow. Most inhibitors are still in clinical stages, and many lack the necessary selectivity and anti-tumor effects. This study aimed to create new inhibitors for the PLK1-PBD by focusing on the PBD binding domain, which has the potential for greater selectivity. A 3D QSAR model was developed using a dataset of 112 compounds to evaluate 500 molecules. ADMET prediction was then used to select three molecules with strong drug-like characteristics. Scaffold hopping was employed to reconstruct 98 new compounds with improved drug-like properties and increased activity. Molecular docking was used to compare the efficient compound abbapolin, confirming the high-activity status of [(14S)-14-hydroxy-14-(pyridin-2-yl)tetradecyl]ammonium,[(14S)-15-(2-furyl)-14-hydroxypentadecyl]ammonium and [(14S)-14-hydroxy-14-phenyltetradecyl]ammonium. Molecular dynamics simulations and MMPBSA were conducted to evaluate the stability of the compounds in the presence of proteins. An in-depth analysis of [(14S)-15-(2-furyl)-14-hydroxypentadecyl]ammonium and [(14S)-14-hydroxy-14-phenyltetradecyl]ammonium identified them as potential candidates for PLK1 inhibitors.

Natural chitosan-based carbon dots as an eco-friendly and effective corrosion inhibitor for mild steel in HCl solution

Polysaccharide chitosan and L-histidine were applied to synthesize chitosan-based carbon dots (CA-CDs) by a simple laser ablation method. After characterization of the CA-CDs by FT-IR, UV-vis, Raman, XRD, TEM, and XPS, the CA-CDs were introduced as an eco-friendly and high-performance corrosion inhibitor for mild steel (MS) in 1.0 M HCl solution. The inhibition action and mechanism of CA-CDs were determined by weight loss and electrochemical measurements, in combination with SEM, AFM, and XPS. The results show that CA-CDs as mixed-type inhibitors could effectively weaken the corrosion of MS in 1.0 M HCl solution, and their maximum inhibition efficiency reaches 97.4 % at 40 mg L-1. The adsorption behavior of CA-CDs well obeys the Langmuir adsorption isotherm containing both chemisorption and physisorption. The chemisorption mainly results from the multiple adsorption sites in the CA-CDs, and the physical adsorption is due to the blocking and barrier effect of CA-CD nanoparticles. Both adsorption behaviors were proposed to elucidate the corrosion inhibition mechanism of CA-CDs.

Prioritization of bioactive compounds envisaging yohimbine as a multi targeted anticancer agent: insight from molecular docking and molecular dynamics simulation

Recently, multi-targeted drugs have attracted much attention in cancer therapy where several therapeutic proteins are targeted by a single agent. Using the published scientific literature, we selected sixteen well-known anticancer targets and seven potential phytobioactive chemicals to find a multitargeted compound by screening through molecular docking. The feasible protein-ligand interaction was further predicted by protein-ligand interaction analysis and molecular dynamic simulation. The phytochemical yohimbine exhibited the lowest docking score in the range of -8.3 to -10.0 kcal/mol over other ligands with all the studied protein targets. Molecular interaction data also revealed the feasible binding of yohimbine with all targets. Moreover, the molecular simulation data also confirmed the stability of protein-ligand complexes with three most scored targets viz. ERK2, PARP1 and PIK3α. Based on our results, yohimbine seems to be the most potent compound out of those selected compounds and can be considered as effective lead molecule against the studied target proteins.Communicated by Ramaswamy H. Sarma.

Origin of Antibiotics and Antibiotic Resistance, and Their Impacts on Drug Development: A Narrative Review

Antibiotics have revolutionized medicine, saving countless lives since their discovery in the early 20th century. However, the origin of antibiotics is now overshadowed by the alarming rise in antibiotic resistance. This global crisis stems from the relentless adaptability of microorganisms, driven by misuse and overuse of antibiotics. This article explores the origin of antibiotics and the subsequent emergence of antibiotic resistance. It delves into the mechanisms employed by bacteria to develop resistance, highlighting the dire consequences of drug resistance, including compromised patient care, increased mortality rates, and escalating healthcare costs. The article elucidates the latest strategies against drug-resistant microorganisms, encompassing innovative approaches such as phage therapy, CRISPR-Cas9 technology, and the exploration of natural compounds. Moreover, it examines the profound impact of antibiotic resistance on drug development, rendering the pursuit of new antibiotics economically challenging. The limitations and challenges in developing novel antibiotics are discussed, along with hurdles in the regulatory process that hinder progress in this critical field. Proposals for modifying the regulatory process to facilitate antibiotic development are presented. The withdrawal of major pharmaceutical firms from antibiotic research is examined, along with potential strategies to re-engage their interest. The article also outlines initiatives to overcome economic challenges and incentivize antibiotic development, emphasizing international collaborations and partnerships. Finally, the article sheds light on government-led initiatives against antibiotic resistance, with a specific focus on the Middle East. It discusses the proactive measures taken by governments in the region, such as Saudi Arabia and the United Arab Emirates, to combat this global threat. In the face of antibiotic resistance, a multifaceted approach is imperative. This article provides valuable insights into the complex landscape of antibiotic development, regulatory challenges, and collaborative efforts required to ensure a future where antibiotics remain effective tools in safeguarding public health.

Virtual screening and molecular dynamics simulation study of abyssomicins as potential inhibitors of COVID-19 virus main protease and spike protein

The lack of any effective cure for the infectious COVID-19 disease has created a sense of urgency and motivated the search for effective antiviral drugs. Abyssomicins are actinomyces-derived spirotetronates polyketides antibiotics known for their promising antibacterial, antitumor, and antiviral activities. In this study, computational approaches were used to investigate the binding mechanism and the inhibitory ability of 38 abyssomicins against the main protease (Mpro) and the spike protein receptor-binding domain (RBD) of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The results identified abyssomicins C, J, W, atrop-O-benzyl abyssomicin C, and atrop-O-benzyl desmethyl abyssomicin C as the most potential inhibitors of Mpro and RBD with binding energy ranges between -8.1 and -9.9 kcal mol-1; and between -6.9 and -8.2 kcal mol-1, respectively. Further analyses of physicochemical properties and drug-likeness suggested that all selected active abyssomicins, with the exception of abyssomicin J, obeyed Lipinski's rule of five. The stability of protein-ligand complexes was confirmed by performing molecular dynamics simulation for 100 ns and evaluating parameters such as such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), total number of contacts, and secondary structure. Prime/MM-GBSA (Molecular Mechanics-General Born Surface Area) and principal component analysis (PCA) analyses also confirmed the stable nature of protein-ligand complexes. Overall, the results showed that the studied abyssomicins have significant interactions with the selected protein targets; therefore, they were deemed viable candidates for further in vitro and in vivo evaluation.Communicated by Ramaswamy H. Sarma.

Metallo-β-lactamase SMB-1 evolves into a more efficient hydrolase under the selective pressure of meropenem

Metallo-β-lactamases (MβLs) are the primary mechanism of resistance to carbapenem antibiotics. To elucidate how MβLs have evolved with the introduction and use of antibiotics, the mutation and evolution of SMB-1 from Serratia marcescens were investigated in microbial evolution plates containing discontinuous meropenem (MEM) concentration gradients. The results revealed 2-point mutations, A242G and S257R; 1 double-site mutation, C240G/E258G; and 3 frameshift mutations, M5, M12, and M13, which are all missense mutations situated at the C-terminus. Compared with that of the wild-type (WT), the minimum inhibitory concentrations (MICs) of MEM for A242G, C240G/E258G, M5, M12, and M13 increased at least 120-fold, and that of S257R increased 8-fold. The catalytic efficiency kcat/Km increased by 365% and 647%, respectively. Concerning the structural changes, the structure at the active site changed from an ordered structure to an unordered conformation. Simultaneously, the flexibility of loop 1 was enhanced. These changes increased the volume of the active site cavity; thus, this was more conducive to exposing the Zn2+ site, facilitating substrate binding and conversion to products. In A242G, structural changes in Gly-242 can be transmitted to the active region via a network of interactions between the side chains of Gly-242 and the amino acid side chains near the active pocket. Together, these results pointed to the process of persistent drug tolerance and resistance, the SMB-1 enzyme evolved into a more exquisite structure with increased flexibility and stability, and stronger hydrolysis activity via genetic mutations and structural changes.

Exploring natural products as multi-target-directed drugs for Parkinson's disease: an in-silico approach integrating QSAR, pharmacophore modeling, and molecular dynamics simulations

Parkinson's disease is a neurodegenerative disorder characterized by the progressive loss of dopaminergic neurons in the midbrain. Current treatments provide limited symptomatic relief without halting disease progression. A multi-targeting approach has shown potential benefits in treating neurodegenerative diseases. In this study, we employed in silico approaches to explore the COCONUT natural products database and identify novel drug candidates with multi-target potential against relevant Parkinson's disease targets. QSAR models were developed to screen for potential bioactive molecules, followed by a hybrid virtual screening approach involving pharmacophore modeling and molecular docking against MAO-B, AA2AR, and NMDAR. ADME evaluation was performed to assess drug-like properties. Our findings revealed 22 candidates that exhibited the desired pharmacophoric features. Particularly, two compounds: CNP0121426 and CNP0242698 exhibited remarkable binding affinities, with energies lower than -10 kcal/mol and promising interaction profiles with the chosen targets. Furthermore, all the ligands displayed desirable pharmacokinetic properties for brain-targeted drugs. Lastly, molecular dynamics simulations were conducted on the lead candidates, belonging to the dihydrochalcone and curcuminoid class, to evaluate their stability over a 100 ns timeframe and compare their dynamics with reference complexes. Our findings revealed the curcuminoid CNP0242698 to have an overall better stability with the three targets compared to the dihydrochalcone, despite the high ligand RMSD, the curcuminoid CNP0242698 showed better protein stability, implying ligand exploration of different orientations. Similarly, AA2AR exhibited higher stability with CNP0242698 compared to the reference complex, despite the high initial ligand RMSD due to the bulkier active site. In NMDAR, CNP0242698 displayed good stability and less fluctuations implying a more restricted conformation within the smaller active site of NMDAR. These results may serve as lead compounds for the development and optimization of natural products as multi-target disease-modifying natural remedies for Parkinson's disease patients. However, experimental assays remain necessary to validate these findings.Communicated by Ramaswamy H. Sarma.

Dopamine modified natural glucomannan as a highly efficient inhibitor for mild steel: Experimental and theoretical methods

In this work, Glucomannan was modified with dopamine to synthesize a new polysaccharide Schiff base (GAD). After confirmation of GAD by NMR and FT-IR spectroscopic methods, it was introduced as a sustainable corrosion inhibitor with excellent anti-corrosion action for mild steel in 0.5 M hydrochloric acid (HCl) solution. Employing electrochemical test, morphology measurement, and theoretical analysis, the anticorrosion performance of GAD on mild steel in 0.5 M HCl solution is determined. Maximum efficiency of GAD for suppressing the corrosion rate of mild steel at 0.12 g L^-1 reaches 99.0 %. After immersion in HCl solution for 24 h, the results from scanning electron microscopy indicate that GAD is firmly attached to the mild steel surface by making a protective layer. According to the X-ray photoelectron spectroscopy (XPS), FeN bonds existed on the steel surface indicate the presence of chemisorption between GAD and Fe to form stable complexes attracted to the active position on the mild steel. The effects of Schiff base groups on the corrosion inhibition efficiencies were also investigated. Moreover, the inhibition mechanism of GAD was further illustrated by the free Gibbs energy, quantum chemical calculation and molecular dynamics simulation.

Revisiting the inhibitory potential of protein kinase inhibitors against NEK7 protein via comprehensive computational investigations

The NEK7 protein is required for spindle formation, cell division, and the activation of the NLRP3 inflammasome receptor. The aberrant expression of NEK7 has been implicated to the growth of metastasis and severe inflammatory conditions like rheumatoid arthritis, liver cirrhosis, and gout. An emergent target for the development of anti-cancer drugs is NEK7. In this context, the PubChem database was used to retrieve the 675 compound library and FDA-approved protein kinase inhibitors, which were then thoroughly examined via in-silico experiments. Computational studies investigated the binding orientation, electronic, and thermodynamic characteristics of drug candidates related to target protein. Drugs were investigated using density functional theory and molecular docking to find binding interactions with NEK7. Molecular dynamic simulations assessed interactions and stability of protein-ligand complex. DFT analyses showed that selected compounds maintained a significant amount of chemical reactivity in both liquid and gaseous states. Alectinib, Crizotinib, and compound 146476703 all displayed promising molecular interactions, according to molecular docking studies, with docking scores of - 32.76, - 30.54, and - 34.34 kJ/mol, respectively. Additionally, MD simulations determined the stability and dynamic characteristics of the complex over a 200 ns production run. The current study's findings indicate that the drugs Alectinib, Crizotinib, and compound 146476703 can successfully inhibit the overexpression of the NEK7 protein. To discover more potent drugs against NEK7, it is recommended to synthesize the derivatives of Alectinib and Crizotinib and carry out additional in-vitro and in-vivo studies at the molecular level.

Optimization of CRISPR-Cas system for clinical cancer therapy

Cancer is a genetic disease caused by alterations in genome and epigenome and is one of the leading causes for death worldwide. The exploration of disease development and therapeutic strategies at the genetic level have become the key to the treatment of cancer and other genetic diseases. The functional analysis of genes and mutations has been slow and laborious. Therefore, there is an urgent need for alternative approaches to improve the current status of cancer research. Gene editing technologies provide technical support for efficient gene disruption and modification in vivo and in vitro, in particular the use of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems. Currently, the applications of CRISPR-Cas systems in cancer rely on different Cas effector proteins and the design of guide RNAs. Furthermore, effective vector delivery must be met for the CRISPR-Cas systems to enter human clinical trials. In this review article, we describe the mechanism of the CRISPR-Cas systems and highlight the applications of class II Cas effector proteins. We also propose a synthetic biology approach to modify the CRISPR-Cas systems, and summarize various delivery approaches facilitating the clinical application of the CRISPR-Cas systems. By modifying the CRISPR-Cas system and optimizing its in vivo delivery, promising and effective treatments for cancers using the CRISPR-Cas system are emerging.

Virtual screening of natural compounds as selective inhibitors of polo-like kinase-1 at C-terminal polo box and N-terminal catalytic domain

The over-expression of Polo-like kinase-1 (PLK1) is associated with cancer prognosis due to its pivotal role in cell proliferation. The N-terminal catalytic domain (NCD) and C-terminal polo box domain (PBD) of PLK1 are critical for the activity of the protein. Drugs that inhibit PLK1 by targeting these domains are on clinical trials, but so far, none has been approved by FDA. Thus, this study targets the two domains of PLK1 to identify compounds with inhibitory potential. Four validated e-pharmacophore models from NCD (PDB ID: 2OU7 and 4J52) and PBD (PDB ID: 5NEI and 5NN2) were used to screen over 26,000 natural compounds from NPASS database. Hits were identified after the well-fitted compounds were subjected to molecular docking study and ADME prediction. The pIC50 and electronic behaviour of the identified hits selectively targeting NCD and PBD of PLK1 were predicted via an externally validated QSAR model and quantum mechanics. The results showed that CAA180504, CAA197326, CAA74619, CAA328856 modulating PLK1 at NCD, and CBB130581, CBB230713, CBB206123, CBB12656 and CBB267117 modulating PLK1 at PBD had better molecular docking scores, pharmacokinetics and drug-like properties than NCD (volasertib) and PBD (purpurogallin) reference inhibitors. The compounds all had satisfactory inhibitory (pIC50) values which range from 6.187 to 7.157. The electronic behaviours of understudied compounds using HOMO/LUMO and global descriptive parameters revealed the atomic portion of the compounds prone to donating and accepting electrons. In conclusion, the hit compounds identified from the library of natural compounds are worthy of further experimental validation.Communicated by Ramaswamy H. Sarma.

Celecoxib, Glipizide, Lapatinib, and Sitagliptin as potential suspects of aggravating SARS-CoV-2 (COVID-19) infection: a computational approach

COVID-19 caused by SARS-CoV-2 has emerged as a potential threat to human life, especially to people suffering from chronic diseases. In this study, we investigated the ability of selected FDA-approved drugs to inhibit TACE (tumor necrosis factor α converting enzyme), which is responsible for the shedding of membrane-bound ACE2 (angiotensin-converting enzyme2) receptors into soluble ACE2. The inhibition of TACE would lead to an increased population of membrane-bound ACE2, which would facilitate ACE2-Spike protein interaction and viral entry. A total of 50 drugs prescribed in treating various chronic diseases in Saudi Arabia were screened by performing molecular docking using AutoDock4.2. Based on docking energy (≤ -9.00 kcal mol^-1), four drugs (Celecoxib, Glipizide, Lapatinib, and Sitagliptin) were identified as potential inhibitors of TACE, with binding affinities up to 10⁶-10⁷ M^-1. Analysis of the molecular docking suggests that these drugs were bound to TACE's catalytic domain and interact with the key residues such as His405, Glu406, and His415, which are involved in active site Zn²⁺ ion chelation. Molecular dynamics simulation was performed to confirm the stability of TACE-drugs complexes. RMSD (root mean square deviation), RMSF (root mean square fluctuation), Rg (radius of gyration), and SASA (solvent accessible surface area) were within the acceptable limits. Free energy calculations using Prime-MM/GBSA suggest that Celecoxib formed the most stable complex with TACE, followed by Glipizide, Sitagliptin, and Lapatinib. The finding of this study suggests a mechanism for drugs to aggravate SARS-CoV-2 infection and hence high mortality in patients suffering from chronic diseases.Communicated by Ramaswamy H. Sarma.

Exploration of the binding between cuminol and bovine serum albumin through spectroscopic, molecular docking and molecular dynamics methods

Cuminol (4-Isopropylbenzyl alcohol), found in the essential oils of several plant sources, is an important constituent of several cosmetics formulations. The interaction of cuminol with model plasma protein bovine serum albumin was studied in this paper. The experimental studies were mainly carried out using fluorescence spectrophotometry aided with UV visible and CD spectroscopies. Intrinsic fluorescence measurements showed that there was a weak binding between cuminol and BSA. The mechanism of binding involved static quenching with around 1:1 binding. The binding was chiefly supported by hydrophobic forces although a little contribution of hydrogen bonding was also found in the interaction and the values of enthalpy change were negative with positive entropy change. The secondary structure of BSA didn't change significantly in presence of low concentrations of cuminol, however, partial unfolding of the former taken place when the concentration of the latter increased. Molecular docking analyses showed cuminol binds at the intersection of subdomains IIA and IIIA, i.e. its binding site is in between Sudlow sites I and II. Molecular dynamics simulations results have shown that BSA forms a stable complex with cuminol and the structure of the former didn't change much in presence of later. Communicated by Ramaswamy H. Sarma.

Efforts in Bioprospecting Research: A Survey of Novel Anticancer Phytochemicals Reported in the Last Decade

Bioprospecting natural products to find prominent agents for medical application is an area of scientific endeavor that has produced many clinically used bioactive compounds, including anticancer agents. These compounds come from plants, microorganisms, and marine life. They are so-called secondary metabolites that are important for a species to survive in the hostile environment of its respective ecosystem. The kingdom of Plantae has been an important source of traditional medicine in the past and is also enormously used today as an exquisite reservoir for detecting novel bioactive compounds that are potent against hard-to-treat maladies such as cancer. Cancer therapies, especially chemotherapies, are fraught with many factors that are difficult to manage, such as drug resistance, adverse side effects, less selectivity, complexity, etc. Here, we report the results of an exploration of the databases of PubMed, Science Direct, and Google Scholar for bioactive anticancer phytochemicals published between 2010 and 2020. Our report is restricted to new compounds with strong-to-moderate bioactivity potential for which mass spectroscopic structural data are available. Each of the phytochemicals reported in this review was assigned to chemical classes with peculiar anticancer properties. In our survey, we found anticancer phytochemicals that are reported to have selective toxicity against cancer cells, to sensitize MDR cancer cells, and to have multitarget effects in several signaling pathways. Surprisingly, many of these compounds have limited follow-up studies. Detailed investigations into the synthesis of more functional derivatives, chemical genetics, and the clinical relevance of these compounds are required to achieve safer chemotherapy.

Identification of a Potential Inhibitor (MCULE-8777613195-0-12) of New Delhi Metallo-β-Lactamase-1 (NDM-1) Using In Silico and In Vitro Approaches

New Delhi metallo-β-lactamase-1 (NDM-1), expressed in different Gram-negative bacteria, is a versatile enzyme capable of hydrolyzing β-lactam rings containing antibiotics such as penicillins, cephalosporins, and even carbapenems. Multidrug resistance in bacteria mediated by NDM-1 is an emerging threat to the public health, with an enormous economic burden. There is a scarcity in the availability of specific NDM-1 inhibitors, and also a lag in the development of new inhibitors in pharmaceutical industries. In order to identify novel inhibitors of NDM-1, we screened a library of more than 20 million compounds, available at the MCULE purchasable database. Virtual screening led to the identification of six potential inhibitors, namely, MCULE-1996250788-0-2, MCULE-8777613195-0-12, MCULE-2896881895-0-14, MCULE-5843881524-0-3, MCULE-4937132985-0-1, and MCULE-7157846117-0-1. Furthermore, analyses by molecular docking and ADME properties showed that MCULE-8777613195-0-12 was the most suitable inhibitor against NDM-1. An analysis of the binding pose revealed that MCULE-8777613195-0-12 formed four hydrogen bonds with the catalytic residues of NDM-1 (His120, His122, His189, and Cys208) and interacted with other key residues. Molecular dynamics simulation and principal component analysis confirmed the stability of the NDM-1 and MCULE-8777613195-0-12 complex. The in vitro enzyme kinetics showed that the catalytic efficiency (i.e., kcat/Km) of NDM-1 on various antibiotics decreased significantly in the presence of MCULE-8777613195-0-12, due to poor catalytic proficiency (kcat) and affinity (Km). The IC50 value of MCULE-8777613195-0-12 (54.2 µM) was comparable to that of a known inhibitor, i.e., D-captopril (10.3 µM). In sum, MCULE-8777613195-0-12 may serve as a scaffold to further design/develop more potent inhibitors of NDM-1 and other β-lactamases.

Antioxidant and antimicrobial potential of two extracts from Capparis spinosa L. and Rumex nervosus and molecular docking investigation of selected major compounds

The present study examined the phytochemical composition, antioxidant, antimicrobial properties, and molecular docking of different solvents extracts (methanol and water) of two medicinal plants, namely, Capparis spinosa L (CS) and Rumex nervosus (RN). Phytochemical analysis showed that total phenol, flavonoids, alkaloids, and vitamin C were significantly (P ≤ 0.05) higher in the methanolic extract of both plants than in other solvents. However, tannin content was significantly (P ≤ 0.05) high in the water extract for both plants. Chloroform and acetone extracts were significantly lower in phytochemicals than other solvents, therefore excluded in this study. GC–MS analysis showed one dominant compound in CS (isopropyl isothiocyanate) and two in RN (pyrogallol and palmitic acid). The antioxidant methods applied (DPPH, ABTS, β-Carotene/linoleic acid assay, and reducing the power) showed that the methanolic extract of CS exerted higher activity in methanolic extract but lower than that of BHA standard. The methanolic extract of both plants inhibited the bacterial pathogens when a minimum inhibitory concentration (MIC) method was applied, compared to water extract with RN-methanolic extract had a lower inhibition concentration than CS-methanolic extract. The molecular interactions study revealed that the palmitic acid and pyrogallol interacted with the receptors' active site. This work concluded that CS and RN showed a remarkable antioxidant and antibacterial effect with the high antimicrobial activity of RN extract.

Substrates and Loaded Iron Ions Relative Position Influence the Catalytic Characteristics of the Metalloenzymes Angelica archangelica Flavone Synthase I and Camellia sinensis Flavonol Synthase

Metalloenzymes are a class of enzymes that catalyze through the metal ions they load. Angelica archangelica flavone synthase I (AnFNS I) and Camellia sinensis flavonol synthase (CaFLS), both of which belong to metalloenzymes, have highly similar structures and metal catalytic cores. However, these two enzymes catalyze the same substrate to produce significantly different products. To identify the cause for the differences in the catalytic characteristics of AnFNS I and CaFLS, their protein models were constructed using homology modeling. Structural alignment and molecular docking was also used to elucidate the molecular basis of the differences observed. To analyze and verify the cause for the differences in the catalytic characteristics of AnFNS I and CaFLS, partial fragments of AnFNS I were used to replace the corresponding fragments on CaFLS, and the catalytic characteristics of the mutants were determined by bioconversion assay in E. coli and in vitro catalytic test. The results suggest that the difference in catalytic characteristics between AnFNS I and CaFLS is caused by the depth of the active pockets and the relative position of the substrate. Mutant 10 which present similar dock result with AnFNS I increased the proportion of diosmetin (a flavone) from 2.54 to 16.68% and decreased the proportion of 4′-O-methyl taxifolin (a flavanol) from 47.28 to 2.88%. It was also indicated that the atoms in the substrate molecule that determine the catalytic outcome may be H-2 and H-3, rather than C-2 and C-3. Moreover, it is speculated that the change in the catalytic characteristics at the changes relative spatial position of H-2/H-3 of hesperetin and the loaded carbonyl iron, caused by charged residues at the entrance of the active pocket, is the key factor for the biosynthesis of flavone from flavanone.

An integrated computational approach to screening of alkaloids inhibitors of TBX3 in breast cancer cell lines

TBX3 is an ancient and evolutionarily conserved family member of T-box transcription factors that acts as a key regulator in embryonic development and organogenesis. It is often overexpressed in various epithelial and mesenchymal malignancies which has a significant impact on various hallmarks of cancer, which mainly includes senescence shunt, apoptosis, anoikis, angiogenesis, and promoting metastatic and expansion of cancer stem cells. In addition to the role of TBX3 in early breast development, a number of studies have also confirmed the amplification of TBX3 in the occurrence and development of breast cancer. To overcome a major challenge in breast cancer treatment, resistance to current anti-cancer drug, it is important to develop new drug pipeline. In this study of different alkaloid molecules, to identify potential alkaloid inhibitors of TBX3, a structure based virtual screening was done involving molecular docking, ADME, toxicity analysis, molecular dynamics simulation. From our study 5 ligands named Jervine, Diflomotecan, Camptothecin, Vincamine, and Anoniane were primarily confirmed as potential inhibitors. The followed screening manner funnels out five potential compounds that have a high scoring function that emphasizes their high binding ability along with no toxicity effects. The molecular mechanics-generalized born surface area (MM-GBSA) and molecular dynamics (MD) simulation showed that Jervine along with Diflomotecan formed the stable complexes with TBX3 which makes it obvious that these two alkaloids can be introduced into the drug development pipeline and used as a new leader to develop new effective drugs against breast cancer.Communicated by Ramaswamy H. Sarma.

Risedronate and Methotrexate Are High-Affinity Inhibitors of New Delhi Metallo-β-Lactamase-1 (NDM-1): A Drug Repurposing Approach

Bacteria expressing New Delhi metallo-β-lactamase-1 (NDM-1) can hydrolyze β-lactam antibiotics (penicillins, cephalosporins, and carbapenems) and, thus, mediate multidrug resistance. The worldwide dissemination of NDM-1 poses a serious threat to public health, imposing a huge economic burden in the development of new antibiotics. Thus, there is an urgent need for the identification of novel NDM-1 inhibitors from a pool of already-known drug molecules. Here, we screened a library of FDA-approved drugs to identify novel non-β-lactam ring-containing inhibitors of NDM-1 by applying computational as well as in vitro experimental approaches. Different steps of high-throughput virtual screening, molecular docking, molecular dynamics simulation, and enzyme kinetics were performed to identify risedronate and methotrexate as the inhibitors with the most potential. The molecular mechanics/generalized Born surface area (MM/GBSA) and molecular dynamics (MD) simulations showed that both of the compounds (risedronate and methotrexate) formed a stable complex with NDM-1. Furthermore, analyses of the binding pose revealed that risedronate formed two hydrogen bonds and three electrostatic interactions with the catalytic residues of NDM-1. Similarly, methotrexate formed four hydrogen bonds and one electrostatic interaction with NDM-1's active site residues. The docking scores of risedronate and methotrexate for NDM-1 were -10.543 kcal mol-1 and -10.189 kcal mol-1, respectively. Steady-state enzyme kinetics in the presence of risedronate and methotrexate showed a decreased catalytic efficiency (i.e., kcat/Km) of NDM-1 on various antibiotics, owing to poor catalytic proficiency and affinity. The results were further validated by determining the MICs of imipenem and meropenem in the presence of risedronate and methotrexate. The IC50 values of the identified inhibitors were in the micromolar range. The findings of this study should be helpful in further characterizing the potential of risedronate and methotrexate to treat bacterial infections.

The Antiproliferative and Apoptotic Effects of a Novel Quinazoline Carrying Substituted-Sulfonamides: In Vitro and Molecular Docking Study

In order to investigate for a new effective and safe anticancer drug, we synthesized a novel series of quinazoline containing biologically active substituted-sulfonamide moiety at 3- position 4a-n. The structure of the newly prepared compounds was proved by microanalysis, IR, ¹H-NMR, ¹³C-NMR and mass spectral data. All the synthesized compounds were evaluated for their in vitro cytotoxic activity in numerous cancer cell lines including A549, HepG-2, LoVo and MCF-7 and normal HUVEC cell line. The two most active compounds 4d and 4f were then tested for their apoptosis induction using DNA content and Annexin V-FITC/PI staining. Moreover, apoptosis initiation was also confirmed using RT-PCR and Western blot. To further understand the binding preferences of quinazoline sulfonamides, docking simulations were used. Among the fourteen new synthesized compounds, we found that compounds 4d and 4f exerted the strongest cytotoxicity against MCF-7 cells with an IC₅₀ value of 2.5 and 5 μM, respectively. Flow cytometry data revealed the ability of compounds 4d and 4f to mediate apoptosis and arrest cell cycle growth at G1 phase. Furthermore, RT-PCR and Western blot results suggested that both 4d and 4f activates apoptotic cell death pathway in MCF-7 cells. Molecular docking assessments indicated that compounds 4d and 4f fit perfectly into Bcl2's active site. Based on the biological properties, we conclude that both compounds 4d and 4f could be used as a new type of anticancer agent, which provides a scientific basis for further research into the treatment of cancer.

Exploring the Binding Pattern of Geraniol with Acetylcholinesterase through In Silico Docking, Molecular Dynamics Simulation, and In Vitro Enzyme Inhibition Kinetics Studies

Acetylcholinesterase (AChE) inhibition is a key element in enhancing cholinergic transmission and subsequently relieving major symptoms of several neurological and neuromuscular disorders. Here, the inhibitory potential of geraniol and its mechanism of inhibition against AChE were elucidated in vitro and validated via an in silico study. Our in vitro enzyme inhibition kinetics results show that at increasing concentrations of geraniol and substrate, Vmax did not change significantly, but Km increased, which indicates that geraniol is a competitive inhibitor against AChE with an IC₅₀ value 98.06 ± 3.92 µM. All the parameters of the ADME study revealed that geraniol is an acceptable drug candidate. A docking study showed that the binding energy of geraniol (−5.6 kcal mol⁻¹) was lower than that of acetylcholine (−4.1 kcal mol⁻¹) with AChE, which exhibited around a 12.58-fold higher binding affinity of geraniol. Furthermore, molecular dynamics simulation revealed that the RMSD of AChE alone or in complex with geraniol fluctuated within acceptable limits throughout the simulation. The mean RMSF value of the complex ensures that the overall conformation of the protein remains conserved. The average values of Rg, MolSA, SASA, and PSA of the complex were 3.16 Å, 204.78, 9.13, and 51.58 Ų, respectively. We found that the total SSE of AChE in the complex was 38.84% (α-helix: 26.57% and β-sheets: 12.27%) and remained consistent throughout the simulation. These findings suggest that geraniol remained inside the binding cavity of AChE in a stable conformation. Further in vivo investigation is required to fully characterize the pharmacokinetic properties, optimization of dose administration, and efficacy of this plant-based natural compound.

Cytotoxicity and molecular docking analysis of racemolactone I, a new sesquiterpene lactone isolated from Inula racemosa

CONTEXT

Traditionally, Inula racemosa Hook. f. (Asteraceae) has been reported to be effective in cancer treatment which motivated the authors to explore the plant for novel anticancer compounds.

OBJECTIVE

To isolate and characterize new cytotoxic phytoconstituents from I. racemosa roots.

MATERIALS AND METHODS

The column chromatography of I. racemosa ethyl acetate extract furnished a novel sesquiterpene lactone whose structure was established by NMR (1D/2D), ES-MS and its cytotoxic properties were assessed on HeLa, MDAMB-231, and A549 cell lines using MTT and LDH (lactate dehydrogenase) assays. Further, morphological changes were analyzed by flow cytometry, mitochondrial membrane potential, AO-EtBr dual staining, and comet assay. Molecular docking and simulation were performed using Glide and Desmond softwares, respectively, to validate the mechanism of action.

RESULTS

The isolated compound was identified as racemolactone I (compound 1). Amongst the cell lines tested, considerable changes were observed in HeLa cells. Compound 1 (IC50 = 0.9 µg/mL) significantly decreased cell viability (82%) concomitantly with high LDH release (76%) at 15 µg/mL. Diverse morphological alterations along with significant increase (9.23%) in apoptotic cells and decrease in viable cells were observed. AO-EtBr dual staining also confirmed the presence of 20% apoptotic cells. A gradual decrease in mitochondrial membrane potential was observed. HeLa cells showed significantly increased comet tail length (48.4 µm), indicating broken DNA strands. In silico studies exhibited that compound 1 binds to the active site of Polo-like kinase-1 and forms a stable complex.

CONCLUSIONS

Racemolactone I was identified as potential anticancer agent, which can further be confirmed by in vivo investigations.

Concatenation of molecular docking and molecular simulation of BACE-1, γ-secretase targeted ligands: in pursuit of Alzheimer's treatment

INTRODUCTION

Alzheimer's disease (AD), the most predominant cause of dementia, has evolved tremendously with an escalating frequency, mainly affecting the elderly population. An effective means of delaying, preventing, or treating AD is yet to be achieved. The failure rate of dementia drug trials has been relatively higher than in other disease-related clinical trials. Hence, multi-targeted therapeutic approaches are gaining attention in pharmacological developments.

AIMS

As an extension of our earlier reports, we have performed docking and molecular dynamic (MD) simulation studies for the same 13 potential ligands against beta-site APP cleaving enzyme 1 (BACE-1) and γ-secretase as a therapeutic target for AD. The In-silico screening of these ligands as potential inhibitors of BACE-1 and γ-secretase was performed using AutoDock enabled PyRx v-0.8. The protein-ligand interactions were analyzed in Discovery Studio 2020 (BIOVIA). The stability of the most promising ligand against BACE-1 and γ-secretase was evaluated by MD simulation using Desmond-2018 (Schrodinger, LLC, NY, USA).

RESULTS

The computational screening revealed that the docking energy values for each of the ligands against both the target enzymes were in the range of -7.0 to -10.1 kcal/mol. Among the 13 ligands, 8 (55E, 6Z2, 6Z5, BRW, F1B, GVP, IQ6, and X37) showed binding energies of ≤-8 kcal/mol against BACE-1 and γ-secretase. For the selected enzyme targets, BACE-1 and γ-secretase, 6Z5 displayed the lowest binding energy of -10.1 and -9.8 kcal/mol, respectively. The MD simulation study confirmed the stability of BACE-6Z5 and γ-secretase-6Z5 complexes and highlighted the formation of a stable complex between 6Z5 and target enzymes.

CONCLUSION

The virtual screening, molecular docking, and molecular dynamics simulation studies revealed the potential of these multi-enzyme targeted ligands. Among the studied ligands, 6Z5 seems to have the best binding potential and forms a stable complex with BACE-1 and γ-secretase. We recommend the synthesis of 6Z5 for future in-vitro and in-vivo studies.

Identification of Novel Drug Candidate for Epithelial Ovarian Cancer via In Silico Investigation and In Vitro Validation

Epithelial ovarian cancer (EOC) has a poor prognosis and high mortality rate; patients are easy to relapse with standard therapies. So, there is an urgent need to develop novel drugs. In this study, differentially expressed genes (DEGs) of EOC were identified in The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Enrichment and protein–protein interaction (PPI) analyses were performed. The drug candidate which has the possibility to treat EOC was predicted by Connectivity Map (CMAP) databases. Moreover, molecular docking was selected to calculate the binding affinity between drug candidate and hub genes. The cytotoxicity of drug candidates was assessed by MTT and colony formation analysis, the proteins coded by hub genes were detected by Western blots, and apoptosis analysis was evaluated by flow cytometry. Finally, 296 overlapping DEGs (|log 2 fold change|>1; q-value <0.05), which were principally involved in the cell cycle (p < 0.05), and cyclin-dependent kinase 1 (CDK1) were screened as the significant hub gene from the PPI network. Furthermore, the 21 drugs were extracted from CMAPs; among them, piperlongumine (PL) showed a lower CMAP score (-0.80, -62.92) and was regarded as the drug candidate. Furthermore, molecular docking results between PL and CDK1 with a docking score of –8.121 kcal/mol were close to the known CDK1 inhibitor (–8.24 kcal/mol). Additionally, in vitro experiments showed that PL inhibited proliferation and induced apoptosis via targeting CDK1 in EOC SKOV3 cells. Our results reveal that PL may be a novel drug candidate for EOC by inhibiting cell cycle.

High-Throughput Screening and Molecular Dynamics Simulation of Natural Product-like Compounds against Alzheimer's Disease through Multitarget Approach

Alzheimer’s disease (AD) is a progressive neurological disorder that affects 50 million people. Despite this, only two classes of medication have been approved by the FDA. Therefore, we have planned to develop therapeutics by multitarget approach. We have explored the library of 2029 natural product-like compounds for their multi-targeting potential against AD by inhibiting AChE, BChE (cholinergic pathway) MAO-A, and MOA-B (oxidative stress pathway) through in silico high-throughput screening and molecular dynamics simulation. Based on the binding energy of these target enzymes, approximately 189 compounds exhibited a score of less than −10 kcal/mol against all targets. However, none of the control inhibitors exhibited a binding affinity of less than −10 kcal/mol. Among these, the top 10 hits of compounds against all four targets were selected for ADME-T analysis. As a result, only F0850-4777 exhibited an acceptable range of physicochemical properties, drug-likeness, pharmacokinetics, and suitability for BBB permeation with high GI-A and non-toxic effects. The molecular dynamics study confirmed that F0850-4777 remained inside the binding cavity of targets in a stable conformation throughout the simulation and Prime-MM/GBSA study revealed that van der Waals’ energy (ΔG_vdW) and non-polar solvation or lipophilic energy (ΔG_{Sol_Lipo}) contribute favorably towards the formation of a stable protein–ligand complex. Thus, F0850-4777 could be a potential candidate against multiple targets of two pathophysiological pathways of AD and opens the doors for further confirmation through in vitro and in vivo systems.

Advanced Computational Methodologies Used in the Discovery of New Natural Anticancer Compounds

Natural chemical compounds have been widely investigated for their programmed necrosis causing characteristics. One of the conventional methods for screening such compounds is the use of concentrated plant extracts without isolation of active moieties for understanding pharmacological activity. For the last two decades, modern medicine has relied mainly on the isolation and purification of one or two complicated active and isomeric compounds. The idea of multi-target drugs has advanced rapidly and impressively from an innovative model when first proposed in the early 2000s to one of the popular trends for drug development in 2021. Alternatively, fragment-based drug discovery is also explored in identifying target-based drug discovery for potent natural anticancer agents which is based on well-defined fragments opposite to use of naturally occurring mixtures. This review summarizes the current key advancements in natural anticancer compounds; computer-assisted/fragment-based structural elucidation and a multi-target approach for the exploration of natural compounds.

Identification of Butyrylcholinesterase and Monoamine Oxidase B Targeted Ligands and their Putative Application in Alzheimer's Treatment: A Computational Strategy

BACKGROUND

With the burgeoning worldwide aging population, the incidence of Alzheimer's disease (AD) and its associated disorders is continuously rising. To appraise other relevant drug targets that could lead to potent enzyme targeting, 13 previously predicted ligands (shown favorable binding with AChE (acetylcholinesterase) and GSK-3 (glycogen synthase kinase) were screened for targeting 3 different enzymes, namely butyrylcholinesterase (BChE), monoamine oxidase A (MAO-A), and monoamine oxidase B (MAO-B) to possibly meet the unmet medical need of better AD treatment.

MATERIALS AND METHODS

The study utilized in silico screening of 13 ligands against BChE, MAO-A and MAOB using PyRx-Python prescription 0.8. The visualization of the active interaction of studied compounds with targeted proteins was performed by Discovery Studio 2020 (BIOVIA).

RESULTS

The computational screening of studied ligands revealed the docking energies in the range of -2.4 to -11.3 kcal/mol for all the studied enzymes. Among the 13 ligands, 8 ligands (55E, 6Z2, 6Z5, BRW, F1B, GVP, IQ6, and X37) showed the binding energies of ≤ -8.0 kcal/mol towards BChE, MAO-A and MAO-B. The ligand 6Z5 was found to be the most potent inhibitor of BChE and MAO-B, with a binding energy of -9.7 and -10.4 kcal mol, respectively. Molecular dynamics simulation of BChE-6Z5 and MAO-B-6Z5 complex confirmed the formation of a stable complex.

CONCLUSION

Our computational screening, molecular docking, and molecular dynamics simulation studies revealed that the above-mentioned enzymes targeted ligands might expedite the future design of potent anti-AD drugs generated on this chemical scaffold.

Recent progress in agents targeting polo-like kinases: Promising therapeutic strategies

Polo-like kinases (PLKs) play important roles in regulating multiple aspects of cell cycle and cell proliferation. In many cancer types, PLK family members are often dysregulated, which can lead to uncontrolled cell proliferation and aberrant cell division and has been shown to associate with poor prognosis of cancers. The key roles of PLK kinases in cancers lead to an enhanced interest in them as promising targets for anticancer drug development. In consideration of PLK inhibitors and some other anticancer agents, such as BRD4, EEF2K and Aurora inhibitors, exert synergy effects in cancer cells, dual-targeting of PLK and other cancer-related targets is regarded as an rational and potent strategy to enhance the effectiveness of single-targeting therapy for cancer treatment. This review introduces the PLK family members at first and then focuses on the recent advances of single-target PLK inhibitors and summarizes the corresponding SARs of them. Moreover, we discuss the synergisms between PLK and other anti-tumor targets, and sum up the current dual-target agents based on them.

Dieckol and Its Derivatives as Potential Inhibitors of SARS-CoV-2 Spike Protein (UK Strain: VUI 202012/01): A Computational Study

The high risk of morbidity and mortality associated with SARS-CoV-2 has accelerated the development of many potential vaccines. However, these vaccines are designed against SARS-CoV-2 isolated in Wuhan, China, and thereby may not be effective against other SARS-CoV-2 variants such as the United Kingdom variant (VUI-202012/01). The UK SARS-CoV-2 variant possesses D614G mutation in the Spike protein, which impart it a high rate of infection. Therefore, newer strategies are warranted to design novel vaccines and drug candidates specifically designed against the mutated forms of SARS-CoV-2. One such strategy is to target ACE2 (angiotensin-converting enzyme2)-Spike protein RBD (receptor binding domain) interaction. Here, we generated a homology model of Spike protein RBD of SARS-CoV-2 UK strain and screened a marine seaweed database employing different computational approaches. On the basis of high-throughput virtual screening, standard precision, and extra precision molecular docking, we identified BE011 (Dieckol) as the most potent compounds against RBD. However, Dieckol did not display drug-like properties, and thus different derivatives of it were generated in silico and evaluated for binding potential and drug-like properties. One Dieckol derivative (DK07) displayed good binding affinity for RBD along with acceptable physicochemical, pharmacokinetic, drug-likeness, and ADMET properties. Analysis of the RBD-DK07 interaction suggested the formation of hydrogen bonds, electrostatic interactions, and hydrophobic interactions with key residues mediating the ACE2-RBD interaction. Molecular dynamics simulation confirmed the stability of the RBD-DK07 complex. Free energy calculations suggested the primary role of electrostatic and Van der Waals' interaction in stabilizing the RBD-DK07 complex. Thus, DK07 may be developed as a potential inhibitor of the RBD-ACE2 interaction. However, these results warrant further validation by in vitro and in vivo studies.

Quinoline yellow dye stimulates whey protein fibrillation via electrostatic and hydrophobic interaction: A biophysical study

Amyloid fibril formation of proteins is associated with a number of neurodegenerative diseases. Several small molecules can accelerate the amyloid fibril formation in vitro and in vivo. However, the molecular mechanism of amyloid fibrillation is still unclear. In this study, we investigated how the food dye quinoline yellow (QY) induces amyloid fibrillation in α-lactalbumin (α-LA), a major whey protein, at pH 2.0. We used several spectroscopy techniques and a microscopy technique to explore how QY provokes amyloid fibrillation in α-LA. From turbidity and Rayleigh light scattering experiments, we found that QY promotes α-LA aggregation in a concentration-dependent manner; the optimal concentration for α-LA aggregation was 0.15 to 10.00 mM. Below 0.1 mM, no aggregation occurred. Quinoline yellow-induced aggregation was a rapid process that escaped the lag phase, but it depended on the concentrations of both α-LA and QY. We also demonstrated that aggregation switched the secondary structure of α-LA from α-helices to cross-β-sheets. We then confirmed the amyloid-like structure of aggregated α-LA by transmission electron microscopy measurements. Molecular docking and simulation confirmed the stability of the α-LA-QY complex due to the formation of 1 hydrogen bond with Lys99 and 2 electrostatic interactions with Arg70 and Lys99, along with hydrophobic interactions with Leu59 and Tyr103. This study will aid in our understanding of how small molecules induce aggregation of proteins inside the stomach (low pH) and affect the digestive process.

Impact of Different Extraction Methods on Furanosesquiterpenoids Content and Antibacterial Activity of Commiphora myrrha Resin

The oleo-gum-resin of Commiphora myrrha is one of the most known natural antimicrobial agents, mainly due to its furanosesquiterpenes. A validated method based on sample extraction by matrix solid-phase dispersion (MSPD) followed by high-performance column chromatography (HPLC) determination is applied to analyze two furanosesquiterpenoids, namely, 2-methoxyfuranodiene (CM-1) and 2-acetoxyfuranodiene (CM-2), existing in C. myrrha. The trial parameters that controlled the extraction prospective were studied and optimized. These include the nature of dispersant, mass ratio of sample to the dispersant, and the volume of elution solvent. A comparative antimicrobial study that used the Minimum Inhibitory Concentration Assay (MIC) method between MSPD, ultrasonic, and Soxhlet of myrrh extracts was also conducted. The optimal MSPD parameters used were (i) 15 mL of methanol applied as elution solvent; (ii) silica gel/sample mass at a 2 : 1 ratio; and (iii) a dispersing sorbent selected as silica gel. Technique retrievals were regulated from 96.87% to 100.54%, with relative standard deviations (RSDs) from 1.24% to 4.45%. Commiphora myrrha-MSPD (CM-MSPD) extract showed the highest antibacterial activity against gram-positive and gram-negative bacteria (156.25 μg/mL and 312.5 μg/mL, respectively) and antifungal activity (156.25 μg/mL). Yields acquired through the MSPD technique were larger than yields from other extraction techniques (sonication and traditional reflux extraction methods) with less consumption of time, sample, and solvent. The mode of antibacterial action of CM-1 and CM-2 was elucidated by performing molecular docking with bacterial DNA gyrase. Both the compounds interacted with key residues of DNA gyrase.

A New Cytotoxic Dimeric Sesquiterpene Isolated from Inula racemosa Hook. f. (Root): In Vitro and In Silico Analyses

A new dimeric sesquiterpene named disesquicin (compound 1) was isolated from Inula racemosa roots by normal-phase MPLC (Medium Pressure Liquid Chromatography), and its structure was established by using extensive spectral analysis. Compound 1, when tested on different human cancer cell lines, showed marked cytotoxic activity (IC50 (µg/mL): 5.99 (MDA-MB), 9.10 (HeLa), and 12.47 (A549)). Docking study revealed that it binds at the catalytic domain of PLK-1 and interacts with catalytic site residues Leu59, Gly60, Lys61, Gly62, Cys67, Ala80, Lys82, Leu130, Arg136, Ser137, Leu139, Glu140, Lys178, Gly180, Asn181, Phe183, and Asp194. The binding of compound 1 to PLK-1 is spontaneous in nature as evident by a free energy of—8.930 kcal mol−1, corresponding to a binding affinity of 3.54 × 106 M−1. Results showed that compound 1 exhibited cytotoxic potential that was further confirmed by in vivo investigations.

Screening of natural compounds for identification of novel inhibitors against β-lactamase CTX-M-152 reported among Kluyvera georgiana isolates: An in vitro and in silico study

Multidrug resistance due to the expression of extended spectrum β-lactamases (ESBLs) by bacterial pathogens is an alarming health concern with huge socio-economic burden. Here, 102 bacterial isolates from Wastewater treatment plants (WTPs) were screened for resistance to different antibiotics. Kirby-Bauer method and phenotypic disc confirmatory test confirmed the prevalence of 20 ESBLs. Polymerase chain reaction-based detection confirmed 11 bla_CTX-M positive bacterial isolates. Genotyping of bacterial isolates by 16S rRNA gene sequencing showed the dissemination of bla_CTX-M in Escherichia fergusonii, Escherichia coli, Shigella sp., Kluyvera georgiana and Enterobacter sp. Amongst Kluyvera georgiana isolates, two were harboring bla_CTX-M-152. The 3D model of CTX-M-152 protein was generated using SwissProt and characterized by Ramachandran plot and SAVES. A library of natural compounds was screened to identify novel CTX-M-152 inhibitor(s). High-throughput virtual screening (HTVS), standard precision (SP) and extra precision (XP) docking led to the identification of five natural compounds (Naringin dihydrochalcone, Salvianolic acid B, Inositol, Guanosine and Ellagic acid) capable of binding to active site of CTX-M-152. Futher, characterization by MM-GBSA (Molecular Mechanism General Born Surface Area), and ADMET (Adsorption, Distribution, Metabolism, Excretion and Toxicity) showed that Ellagic acid was the most potent inhibitor of CTX-M-152. Molecular dynamics simulation also confirmed that Ellagic acid form a stable complex with CTX-M-152. The ability of Ellagic acid to inhibit growth of bacteria harboring CTX-M-152 was confirmed by MIC (Minimum Inhibitory Concentration; broth dilution method) and Zone of Inhibition (ZOI) studies with respect to Cefotaxime. The identification of a novel inhibitor of CTX-M-152 from a natural source holds promise for employment in the control of bacterial infections.

Cationic gemini surfactant stimulates amyloid fibril formation in bovine liver catalase at physiological pH. A biophysical study

Surfactant molecules stimulate amyloid fibrillation and conformational switching in proteins but the mechanisms by which they accomplish these effects are unclear. A cationic gemini surfactant, C₁₆C₄C₁₆Br₂, with two positively charged heads and two-16C hydrophobic tails induces the amyloid fibrillation of bovine liver catalase (BLC) in vitro at physiological pH. The BLC transformed into amyloid aggregates in the presence of low concentrations (2–150 μM) of C₁₆C₄C₁₆Br₂ at pH 7.4, as confirmed by the use of several biophysical techniques (Rayleigh light scattering (RLS), intrinsic fluorescence, thioflavin T fluorescence (ThT), far-UV circular dichroism, and transmission electron microscopy). The secondary structure of BLC also changed according to the concentration of C₁₆C₄C₁₆Br₂: the α-helical structure of BLC decreased in the presence of 2–100 μM of C₁₆C₄C₁₆Br₂ but at concentrations above 200 μM BLC regained a α-helical structure very similar to the native BLC. In silico molecular docking between BLC and C₁₆C₄C₁₆Br₂ suggest that the positively charged heads of the surfactant interact with Asp127 through attractive electrostatic interactions. Moreover, a Pi-cation electrostatic interaction and hydrophobic interactions also take place between the tails of the surfactant and BLC. The stability of the BLC–C₁₆C₄C₁₆Br₂ complex was confirmed by performing a molecular dynamics simulation and evaluating parameters such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (R_g), and solvent accessible surface area (SASA). Apart from its aggregation inducing properties, the gemini surfactant itself causes toxicity to the cancerous cell (A549): which is confirmed by MTT assay. This work delivers new insight into the effect of cationic gemini surfactants in amyloid aggregation and paves the way to the rational design of new anti-amyloidogenic agents.

Surfactant molecules stimulate amyloid fibrillation and conformational switching in proteins but the mechanisms by which they accomplish these effects are unclear.

Inhibitory potential of repurposed drugs against the SARS-CoV-2 main protease: a computational-aided approach

The exponential increase in cases and mortality of coronavirus disease (COVID-19) has called for a need to develop drugs to treat this infection. Using in silico and molecular docking approaches, this study investigated the inhibitory effects of Pradimicin A, Lamivudine, Plerixafor and Lopinavir against SARS-CoV-2 M^pro. ADME/Tox of the ligands, pharmacophore hypothesis of the co-crystalized ligand and the receptor, and docking studies were carried out on different modules of Schrodinger (2019-4) Maestro v12.2. Among the ligands subjected to ADME/Tox by QikProp, Lamivudine demonstrated drug-like physico-chemical properties. A total of five pharmacophore binding sites (A3, A4, R9, R10, and R11) were predicted from the co-crystalized ligand and the binding cavity of the SARS-CoV-2 M^pro. The docking result showed that Lopinavir and Lamivudine bind with a higher affinity and lower free energy than the standard ligand having a glide score of -9.2 kcal/mol and -5.3 kcal/mol, respectively. Plerixafor and Pradimicin A have a glide score of -3.7 kcal/mol and -2.4 kcal/mol, respectively, which is lower than the co-crystallized ligand with a glide score of -5.3 kcal/mol. Molecular dynamics confirmed that the ligands maintained their interaction with the protein with lower RMSD fluctuations over the trajectory period of 100 nsecs and that GLU166 residue is pivotal for binding. On the whole, present study specifies the repurposing aptitude of these molecules as inhibitors of SARS-CoV-2 M^pro with higher binding scores and forms energetically stable complexes with M^pro.Communicated by Ramaswamy H. Sarma.

Siphonocholin isolated from red sea sponge Siphonochalina siphonella attenuates quorum sensing controlled virulence and biofilm formation

Increasing incidence of multi-drug resistant bacterial pathogens, especially in clinical settings, has been developed into a grave health situation. The drug resistance problem demands the necessity for alternative unique therapeutic policies. One such tactic is targeting the quorum sensing (QS) controlled virulence and biofilm production. In this study, we evaluated a marine steroid Siphonocholin (Syph-1) isolated from Siphonochalina siphonella against Chromobacterium violaceum (CV) 12472, Pseudomonas aeruginosa (PAO1), Methicillin-resistant Staphylococcus aureus (MRSA) and Acinetobacter baumannii (BAA) for biofilm and pellicle formation inhibition, and anti-QS property. MIC of Syph-1 against MRSA, CV, PAO1 was found as 64 µg/mL and 256 µg/mL against BAA. At selected sub-MICs, Syph-1 significantly (P ≤ 0.05) decreased the production of QS regulated virulence functions of CV12472 (violacein) and PAO1 [elastase, total protease, pyocyanin, chitinase, exopolysaccharides, and swarming motility]. The Syph-1 significantly decreased (p = 0.005) biofilm formation ability of tested bacterial pathogens, at sub-MIC level (PAO1 > MRSA > CV > BAA) and pellicle formation in A. baumannii (at 128 µg/mL). Molecular docking and simulation results indicated that Siph-1 was bound at the active site of BfmR N-terminal domain with high affinity. This study highlights the anti-QS and anti-biofilm activity of Syph-1 against bacterial pathogens reflecting its broad spectrum anti-infective potential.

Virtual Screening of FDA-Approved Drugs against LasR of Pseudomonas aeruginosa for Antibiofilm Potential

Pseudomonas aeruginosa is a Gram-negative pathogenic bacterium that is present commonly in soil and water and is responsible for causing septic shock, pneumonia, urinary tract and gastrointestinal infections, etc. The multi-drug resistance (MDR) phenomenon has increased dramatically in past years and is now considered a major threat globally, so there is an urgent need to develop new strategies to overcome drug resistance by P. aeruginosa. In P. aeruginosa, a major factor of drug resistance is associated to the formation of biofilms by the LasR enzyme, which regulates quorum sensing and has been reported as a new therapeutic target for designing novel antibacterial molecules. In this study, virtual screening and molecular docking were performed against the ligand binding domain (LBD) of LasR by employing a pharmacophore hypothesis for the screening of 2373 FDA-approved compounds to filter top-scoring hit compounds. Six inhibitors out of 2373 compounds were found to have binding affinities close to that of known LasR inhibitors. The binding modes of these compounds to the binding site in LasR-LBD were analyzed to identify the key interactions that contribute to the inhibition of LasR activity. Then, 50 ns simulations of top hit compounds were performed to elucidate the stability of their binding conformations with the LasR-LBD. This study, thus concluded that sulfamerazine showed the highest binding affinity for the LasR-LBD binding pocket exhibiting strong inhibitory binding interactions during molecular dynamics (MD) simulation.