Molecular Modeling of Surfactant Micellization Using Solvent-Accessible Surface Area

Functional analysis, virtual screening, and molecular dynamics revealed potential novel drug targets and their inhibitors against cardiovascular disease in human

Cardiovascular disease (CVD) is a group of diseases, affecting the human heart and accounting for 30% of deaths worldwide. Major CVDs include heart failure, hypertension, stroke, etc. Various therapeutics are available against CVD, still there is a dire need to find out potential protein drug targets to reduce economic burden and mortality rate. Goal of the current study was to utilize sequential computational techniques to find the best cardiovascular drug targets and their inhibitors. Common human cardiovascular targets of both databases (GeneCards and Uniprot) were subjected to bioinformatics analyses. Purpose was to validate putative therapeutic targets employing the structure-based bioinformatics methods to determine their physiochemical properties and biological processes. Three stable proteins, that have 0 transmembrane helices, and possess biological processes were screened as potential protein-based therapeutic targets: Hemoglobin subunit beta (HBB), Gamma-enolase (ENO2), and Cholesteryl ester transfer protein (CETP). Tertiary structures of target proteins were retrieved from PDB, and molecular docking technique was utilized to evaluate a library of 5000 phytochemicals against the interacting residues of the target protein as well as their respective standard drugs through MOE and Pyrx software. Top five phytochemicals (d-Sesamin, 1,3-benzodioxole, Sativanone, Thiamine, and Cajanol) were identified based on their RMSD and docking scores as compared to their standard drugs. The docking studies were also validated by MM-GBSA binding free energy and molecular dynamics simulations. According to the study's findings, these phytochemicals may eventually be used as drugs to treat CVD. Further in vitro testing is required to confirm their efficacy and drug potency.Communicated by Ramaswamy H. Sarma.

Molecular interaction and MD-simulations: investigation of Sizofiran as a promising anti-cancer agent targeting eIF4E in colorectal cancer

CRC has a major global health impact due to high mortality rates. CRC shows high expression of eukaryotic translation initiation factor (eIF4E) protein, the rapid development of lung, bladder, colon, prostate, breast, head, and neck cancer is attributed to the dysregulation of eIF4E making an important target for treatment. Targeting eIF4E-mediated translation is a promising anti-cancer strategy. Many organic compounds that inhibit eIF4E are being studied clinically. The compound Sizofiran has emerged as a promising eIF4E inhibitor candidate, but its exact mechanism of action is unclear. In an effort to close this discrepancy by clarifying the mechanism of the interactions between phytochemical substances and eIF4E, molecular docking and dynamics studies were conducted. Molecular docking studies found Sizofiran (- 12.513 kcal/mol) has the most affinity eIF4E binding energy out of 93 phytochemicals, 5 current drugs, and 4 known inhibitors. This positions it as a top eIF4E inhibitor candidate. An alignment of eIF4E protein sequences from multiple pathogens revealed that the glutamate103 interacting residues are evolutionarily conserved across the different eIF4E proteins. Further insights from 100 ns of MD simulations supported Sizofiran having superior stability and eIF4E inhibition compared to reference compounds. Designed Sizofiran-related compounds showed better activity than the current drugs such as Camptosar, Sorafenib, Regorafenib, Doxorubicin, and Kenpaullone, indicating strong potential to suppress CRC progression by targeting eIF4E. This research aims to significantly aid development of improved eIF4E-targeting drugs for cancer treatment.

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Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-024-00206-3.

Relationship of single and co-exposure of per-and polyfluoroalkyl substances and their alternatives with uric acid: A community-based study in China

Numerous studies have suggested per-and polyfluoroalkyl substances (PFASs) are related to uric acid levels, but evidence related to PFAS alternatives is limited. Moreover, the effect of the combined exposure to PFASs and their alternatives on uric acid has not been reported. Hence, we conducted a cross-sectional study involving 1312 adults in Guangzhou, China. Generalized linear regression model was adopted to explore the effect of single PFAS exposure on serum uric acid levels. Further, multi-pollutant models such as Bayesian kernel machine regression, weighted quantile sum, and quantile G-computation were employed to investigate the combined association of PFASs and alternatives with serum uric acid levels. We performed molecular docking to understand the potential interaction of PFAS with Organic Anion Transporters (OATs), involved in the secretion of uric acid. Per log serum 6:2 Cl-PFESA and PFOA increases were accompanied with an increase of serum uric acid with statistical significance (for 6:2 Cl-PFESA: beta: 0.19 ng/mL, 95% CI 0.11-0.26 and for PFOA: beta: 0.43 ng/mL, 95% CI 0.34-0.52). The associations were strongest among overweight and elderly. Multi-pollutant models also revealed a positive association. These positive associations may be PFASs can competitively combine with OAT1 and OAT3, leading to the increase of serum uric acid.

Molecular dynamics investigation on synthesis of a pH- and temperature-sensitive carbon nanotube loaded with doxorubicin

The many exotic properties of carbon nanotubes (CNTs) make them a powerful attraction in the field of drug delivery systems (DDS). In this work, based on quantum chemical calculation and molecular simulation techniques, polyacrylic acid (PAA) and N-isopropyl acrylamide (NIP) are selected and acted simultaneously on the CNT to form a stable system (FCNT). As a potential DDS, FCNT captures the dispersed doxorubicin (DOX) molecules around it and maintains a stable configuration. In these processes, electrostatic and van der Waals forces act synergistically, with van der Waals forces dominating. Compared to NIP, PAA molecules exhibit stronger adhesion and encapsulation efficiency to CNT and stronger adsorption capacity to DOX. This study reveals the mechanism of action among PAA, NIP, CNT, and DOX, providing feasibility verification and prospective guidance for the experimental synthesis of PAA-NIP-CNT-type multifunctional DDS, and also broadening the idea for exploring more efficient DDS suitable for DOX.

In silico discovery of potential sodium-glucose cotransporter-2 inhibitors from natural products for treatment of heart failure via molecular docking and molecular dynamics simulation approach

Heart failure (HF) is the end stage of cardiovascular disease. Because of its complex condition and poor prognosis, HF has become an important public health problem in the world. Sodium-glucose cotransporter-2 (SGLT2) is a member of the glucose transporter family. Recently, SGLT2 inhibitors have been applied to treat HF. In this study, the main aim was to discover natural SGLT2 inhibitor from Chinese herbs through docking-based virtual screening. Totally 113 natural compounds of potential SGLT2 inhibitor were identified, which displayed docking affinity higher than six approved inhibitors (dapagliflozin (IC50 = 4.9 nM), canagliflozin (IC50 = 4.4 nM 6.7), ipragliflozin (IC50 = 7.4 nM), empagliflozin (IC50 = 3.1 nM), tofogliflozin (IC50 = 4 nM) and luseogliflozin (IC50 = 2.3 nM)) through docking-based virtual screening. Then, the top three hits (ZINC70455591, ZINC85594065 and ZINC14588133) and six known inhibitors were selected for molecular dynamics simulation and the binding free energy calculation using molecular mechanics Poisson-Boltzmann surface area to demonstrate the stability and affinity of docked complexes. These results pointed out that the three docked complexes were stabilized and the chosen compounds were tightly adhering to the binding site of SGLT2. Besides, pharmacokinetic properties of the selected compounds showed those natural compounds may be potential drug candidates. This study may be contributed to further in vitro and in vivo validation and the development of novel SGLT2 inhibitor for treating HF.Communicated by Ramaswamy H. Sarma.

Computational formulation study of insulin on biodegradable polymers

Insulin administered orally has a limited therapeutic profile due to factors such as digestion enzymes, pH, temperature, and acidic conditions in the gastrointestinal tract. Type 1 diabetes patients are typically restricted to use intradermal insulin injections to manage their blood sugar levels as oral administration is not available. Research has shown that polymers could enhance the oral bioavailability of therapeutic biologicals, but traditional methods for developing suitable polymers are time-consuming and resource-intensive. Although computational formulations can be used to identify the best polymers more quickly. The true potential of biological formulations has not been fully explored due to a lack of benchmarking studies. Therefore, molecular modelling techniques were used as a case study in this research to determine which polymer is most compatible among five natural biodegradable polymers to address insulin stability. Specially, molecular dynamics simulations were conducted in order to compare insulin-polymer mixtures at different pH levels and temperatures. Hormonal peptide morphological properties were analyzed in body and storage conditions to assess stability of insulin with and without polymers. According to our computational simulations and energetic analyses, polymer cyclodextrin and chitosan maintain insulin stability the most effectively, while alginate and pectin are less effective relatively. Overall, this study contributes valuable insight into the role of biopolymers in stabilizing hormonal peptides in biological and storage conditions. A study such as this could have a significant impact on the development of new drug delivery systems and encourage scientists to utilize them in the formulation of biologicals.

Integrated approach for studying bioactive compounds from Cladosporium spp. against estrogen receptor alpha as breast cancer drug target

Cladosporium spp. have been reported for their great diversity of secondary metabolites which represent as a prominent base material for verifying the biological activities. Several bioactive compounds which have antimicrobial, cytotoxic, quorum sensing inhibitory and phytotoxic activities have been isolated from Cladosporium species. Most of them are still needed to be explored for their anticancer properties. Therefore, the present study is focused on screening and identifying the bioactive compounds of Cladosporium spp. for their anticancer activity via the integrated approaches of Molecular Docking (MD), Molecular Dynamics Simulation (MDS) and Density Functional Theory (DFT) studies. A total of 123 bioactive compounds of Cladosporium spp. were explored for their binding affinity with the selected breast cancer drug target receptor such as estrogen receptor alpha (PDB:6CBZ). The Molecular Docking studies revealed that amongst the bioactive compounds screened, Altertoxin X and Cladosporol H showed a good binding affinity of - 10.5 kcal/mol and - 10.3 kcal/mol, respectively, with the estrogen receptor alpha when compared to the reference compound (17[Formula: see text]-Estradiol: - 10.2 kcal/mol). The MDS study indicated the stable binding patterns and conformation of the estrogen receptor alpha-Altertoxin X complex in a stimulating environment. In addition, in silico absorption, distribution, metabolism, excretion and toxicity (ADMET) study suggested that Altertoxin X has a good oral bioavailability with a high LD[Formula: see text] value of 2.375 mol/kg and did not cause any hepatotoxicity and skin sensitization. In summary, the integrated approaches revealed that Altertoxin X possesses a promising anticancer activity and could serve as a new therapeutic drug for breast cancer treatment.

In-silico study of reducing human health risk of POP residues' direct (from tea) or indirect exposure (from tea garden soil): Improved rhizosphere microbial degradation, toxicity control, and mechanism analysis

The accumulation of potentially harmful substances in tea garden soils and tea leaves, especially persistent organic pollutants (POPs), is a special concern for tea consumers worldwide. However, their potential health and ecological risks in tea gardens have rarely been investigated. This study proposed measures to improve the degradation ability of POPs by the tea rhizosphere and to reduce the human health risks caused by POPs after tea consumption. In this study, the binding energy values of six types of POPs and the degraded protein were used to reflect the degradation ability and calculated using molecular dynamic simulations. The main root secretions (i.e., catechin, glucose, arginine, and oxalic acid) were selected and applied with a combination of tea fertilizer and trace element combination (i.e., urea, straw, and copper element), leading to an improved degradation ability (49.59 %) of POPs. To investigate the mechanisms of the factors that affect the degradation ability, molecular docking, tensor singular value decomposition methods, multivariate correlation analysis and 2D-QSAR model were used. The results showed that the solvation energy and solvent accessible surface area are the main forces, and the molecular weight, boiling point, and topological radius of the POPs were the key molecular features affecting their degradation ability. Based on the three key characteristics, a diet avoidance scheme (i.e., avoiding lysine, maslinic acid, ethanol, perfluorocaproic acid, and cholesterol with tea), which can reduce the binding ability of POP residues to aromatic hydrocarbon receptors by 506.13 %. This work will provide theoretical strategies to improve the quality and safety of tea production and reduce the potential risks of harmful substance residues in tea garden soils and tea leaves.

Naringenin as a potential inhibitor of human cyclin-dependent kinase 6: Molecular and structural insights into anti-cancer therapeutics

Cancer is one of the major causes of global deaths and needs immediate therapeutic development. So far, several strategies have been undertaken to prevent cancer, including kinase targeting by small-molecule inhibitors. Cyclin dependent kinase 6 (CDK6) plays an essential role in cancer progression and development as its overexpression is associated with tumor development and progression. The present study demonstrated that Naringenin (NAG) binds strongly to CDK6 with a binding affinity of -7.51 kcal/mol. ATPase assay of CDK6 in the presence of NAG shows that it inhibits CDK6 with an IC₅₀ = 3.13 μM. Fluorescence and isothermal titration calorimetry studies demonstrated that NAG binds to CDK6 with the binding constant (K) values of 3.55 × 10⁶ M^-1 and 7.06 ± 2.70 × 10⁶ M^-1, respectively. The cell-based functional studies showed that NAG decreases the cell viability of human cancer cell lines, induces apoptosis, and reduces their colonization ability. Outcomes of the present in silico and in vitro studies highlighted the significance of NAG for the development of anti-cancer leads in terms of CDK6 inhibitors and provided future implications for combinatorial anti-cancer therapies.

Triazole Derivatives Target 14α-Demethylase (LDM) Enzyme in Candida albicans Causing Ergosterol Biosynthesis Inhibition

Candida albicans is the most dominant and prevalent cause of fungal infections in humans. Azoles are considered as first-line drugs for the treatment of these infections. However, their prolonged and insistent use has led to multidrug resistance and treatment failures. To overcome this, modification or derivatization of the azole ring has led to the development of new and effective antifungal molecules. In a previous study, we reported on the development of new triazole-based molecules as potential antifungal agents against Candida auris. In this study, the most potent molecules from the previous study were docked and simulated with lanosterol 14-alpha demethylase enzyme. These compounds were further evaluated for in vitro susceptibility testing against C. albicans. In silico results revealed favorable structural dynamics of the compounds, implying that the compounds would be able to effectively bind to the target enzyme, which was further manifested by the strong interaction of the test compounds with the amino acid residues of the target enzyme. In vitro studies targeting quantification of ergosterol content revealed that pta1 was the most active compound and inhibited ergosterol production by >90% in both drug-susceptible and resistant C. albicans isolates. Furthermore, RT-qPCR results revealed downregulation of ERG11 gene when C. albicans cells were treated with the test compound, which aligns with the decreased ergosterol content. In addition, the active triazole derivatives were also found to be potent inhibitors of biofilm formation. Both in silico and in vitro results indicate that these triazole derivatives have the potential to be taken to the next level of antifungal drug development.

Structure-based identification of potential SARS-CoV-2 main protease inhibitors

To address coronavirus disease (COVID-19), currently, no effective drug or vaccine is available. In this regard, molecular modeling approaches are highly useful to discover potential inhibitors of the main protease (Mpro) enzyme of SARS-CoV-2. Since, the Mpro enzyme plays key roles in mediating viral replication and transcription; therefore, it is considered as an attractive drug target to control SARS-CoV-2 infection. By using structure-based drug design, pharmacophore modeling, and virtual high throughput drug screening combined with docking and all-atom molecular dynamics simulation approach, we have identified five potential inhibitors of SARS-CoV-2 Mpro. MD simulation studies revealed that compound 54035018 binds to the Mpro with high affinity (ΔGbind -37.40 kcal/mol), and the complex is more stable in comparison with other protein-ligand complexes. We have identified promising leads to fight COVID-19 infection as these compounds fulfill all drug-likeness properties. However, experimental and clinical validations are required for COVID-19 therapy.Communicated by Ramaswamy H. Sarma.

Coarse-Grained Molecular Dynamics Simulations of Paclitaxel-Loaded Polymeric Micelles

A continuous manufacturing technology based on coaxial turbulent jet in coflow was previously developed to produce paclitaxel-loaded polymeric micelles. Herein, coarse-grained molecular dynamics (CG-MD) simulations were implemented to better understand the effect of the material attributes (i.e., the drug-polymer ratio and the ethanol concentration) and process parameters (i.e., temperature) on the self-assembly process of polymeric micelles as well as to provide molecular details on micelle instability. An all-atom (AA) poly (ethylene glycol)-poly (lactic acid) (PEG-PLA) polymer model was developed as the reference for parameterizing a coarse-grained (CG) model, and the AA polymer model was further validated with experimental glass transition temperature (T_g). The model transferability was verified by comparing structural properties between the AA and CG models. The CG model was further validated with experimental data, including micelle particle size measurements and drug encapsulation efficiency. Furthermore, the encapsulation of paclitaxel into the polymeric micelles was included in the simulations, taking into consideration the interactions between the paclitaxel and the polymers. The results from various points of view demonstrated a strong dependence of the shape of the micelles on the drug encapsulation, with micelles transitioning from spherical to ellipsoidal structures with an increasing paclitaxel amount. Simulation data were also used to identify the critical aggregation number (i.e., the number of polymer and drug molecules required for transition from one shape to another). Improved micellar structural stability was found with a larger micellar size and less solvent accessibility. Lastly, an evaluation was performed on the micellar dissociation free energy using a steered molecular dynamics simulation over a range of temperatures and ethanol concentrations. These simulations revealed that at higher ethanol and temperature conditions, micelles become destabilized, resulting in greater paclitaxel release. The increased drug release was determined to originate from the solvation of the hydrophobic core, which promoted micellar swelling and an associated reduction in hydrophobic interactions, leading to a loosely packed micellar structure.

Malachite Green, the hazardous materials that can bind to Apo-transferrin and change the iron transfer

Different groups of synthetic dyes might lead to environmental pollution. The binding affinity among hazardous materials with biomolecules necessitates a detailed understanding of their binding properties. Malachite Green might induce a change in the iron transfer by Apo-transferrin. Spectroscopic studies showed malachite green oxalate (MGO) could form the apo-transferrin-MGO complex and change the Accessible Surface Area (ASA) of the key amino acids for iron transfer. According to the ASA results the accessible surface area of Tyrosine, Aspartate, and Histidine of apo-transferrin significantly were changed, which can be considered as a convincing reason for changing the iron transfer. Moreover, based on the fluorescence data MGO could quench the fluorescence intensity of apo-transferrin in a static quenching mechanism. The experimental and Molecular Dynamic simulation results represented that the binding process led to micro environmental changes, around tryptophan residues and altered the tertiary structure of apo-transferrin. The Circular Dichroism (CD) spectra result represented a decrease in the amount of the α-Helix, as well as, increase in the β-sheet volumes of the apo-transferrin structure. Moreover, FTIR spectroscopy results showed a hypochromic shift in the peaks of amide I and II. Molecular docking and MD simulation confirmed all the computational findings.

MAP/Microtubule Affinity Regulating Kinase 4 Inhibitory Potential of Irisin: A New Therapeutic Strategy to Combat Cancer and Alzheimer's Disease

Irisin is a clinically significant protein playing a valuable role in regulating various diseases. Irisin attenuates synaptic and memory dysfunction, highlighting its importance in Alzheimer's disease. On the other hand, Microtubule Affinity Regulating Kinase 4 (MARK4) is associated with various cancer types, uncontrolled neuronal migrations, and disrupted microtubule dynamics. In addition, MARK4 has been explored as a potential drug target for cancer and Alzheimer's disease therapy. Here, we studied the binding and subsequent inhibition of MARK4 by irisin. Irisin binds to MARK4 with an admirable affinity (K = 0.8 × 107 M-1), subsequently inhibiting its activity (IC50 = 2.71 µm). In vitro studies were further validated by docking and simulations. Molecular docking revealed several hydrogen bonds between irisin and MARK4, including critical residues, Lys38, Val40, and Ser134. Furthermore, the molecular dynamic simulation showed that the binding of irisin resulted in enhanced stability of MARK4. This study provides a rationale to use irisin as a therapeutic agent to treat MARK4-associated diseases.

Impact of single amino acid substitution on the structure and function of TANK-binding kinase-1

Tank-binding kinase 1 (TBK1) is a serine/threonine protein kinase involved in various signaling pathways and subsequently regulates cell proliferation, apoptosis, autophagy, antiviral and antitumor immunity. Dysfunction of TBK1 can cause many complex diseases, including autoimmunity, neurodegeneration, and cancer. This dysfunction of TBK1 may result from single amino acid substitutions and subsequent structural alterations. This study analyzed the effect of substituting amino acids on TBK1 structure, function, and subsequent disease using advanced computational methods and various tools. In the initial assessment, a total of 467 mutations were found to be deleterious. After that, in detailed structural and sequential analyses, 13 mutations were found to be pathogenic. Finally, based on the functional importance, two variants (K38D and S172A) of the TBK1 kinase domain were selected and studied in detail by utilizing all-atom molecular dynamics (MD) simulation for 200 ns. MD simulation, including correlation matrix and principal component analysis, helps to get deeper insights into the TBK1 structure at the atomic level. We observed a substantial change in variants' conformation, which may be possible for structural alteration and subsequent TBK1 dysfunction. However, substitution S172A shows a significant conformational change in TBK1 structure as compared to K38D. Thus, this study provides a structural basis to understand the effect of mutations on the kinase domain of TBK1 and its function associated with disease progression.

Critical Micelle Concentrations in Surfactant Mixtures and Blends by Simulation

We explore the use of coarse-grained dissipative particle dynamics simulations to predict critical micelle concentrations (CMCs) in polydisperse surfactant mixtures and blends. By fitting pseudo-phase separation models (PSMs) to aqueous solutions of binary surfactant mixtures at selected compositions above the CMC, we avoid the need for expensive simulations of more complex multicomponent mixtures performed as a function of dilution. The approach is demonstrated for sodium laureth sulfate (SLES) surfactants with polydispersity in the ethoxylate spacer. For this system, we find a modest degree of cooperativity in micelle formation, which we attribute to the reduced repulsion between charged headgroups for surfactants with dissimilar ethoxylate spacer lengths. However, this is insufficient to explain the lowered CMC often observed in commercial SLES samples, which we attribute to the presence of small amounts of unsulfated alkyl ethoxylates and/or traces of salt.

Finite-Size Effects and Optimal System Sizes in Simulations of Surfactant Micelle Self-Assembly

The spontaneous formation of micelles in aqueous solutions is governed by the amphipathic nature of surfactants and is practically interesting due to the regular use of micelles as membrane mimics, for the characterization of protein structure, and for drug design and delivery. We performed a systematic characterization of the finite-size effect observed in single-component dodecylphosphocholine (DPC) micelles with the coarse-grained MARTINI model. Of multiple coarse-grained solvent models investigated using large system sizes, the nonpolarizable solvent model was found to most accurately reproduce SANS spectra of 100 mM DPC in aqueous solution. We systematically investigated the finite-size effect at constant 100 mM concentration in 23 systems of sizes 40-150 DPC, confirming the finite-size effect to manifest as an oscillation in the mean micelle aggregation number about the thermodynamic aggregation number as the system size increases. The oscillations in aggregation number mostly diminish once the system supports the formation of three micelles. Similar oscillations were observed in the estimated critical micelle concentration with a mean value of 1.10 mM, which is in agreement with experiment to 0.1 mM. The accuracy of using a multiscale simulation approach to avoid finite-size effects in the micelle size distribution and SANS spectra using MARTINI and CHARMM36 was explored using multiple long time scale 500 DPC coarse-grained simulations, which were back-mapped to CHARMM36 all-atom systems. It was found that the MARTINI model generally occupies more volume than the all-atom model, leading to the formation of micelles that are of a reasonable radius of gyration but are smaller in aggregation number. The systematic characterization of the finite-size effect and exploration of multiscale modeling presented in this work provide guidance for the accurate modeling of micelles in simulations.

Impact of non-synonymous mutations on the structure and function of telomeric repeat binding factor 1

Telomeric repeat binding factor 1 (TRF1) is one of the major components of the shelterin complex. It directly binds to the telomere and controls its function by regulating the telomerase acting on it. Several variations are reported in the TRF1 gene; some are associated with variety of diseases. Here, we have studied the structural and functional significance of these variations in the TRFH domain of TRF1. We have used cutting-edge computational methods such as SIFT, PolyPhen-2, PROVEAN, Mutation Assessor, mCSM, SDM, STRUM, MAESTRO, and DUET to predict the effects of 124 mutations in the TRFH domain of TRF1. Out of 124 mutations, we have identified 12 deleterious mutations with high confidence based on their prediction. To see the impact of the finally selected mutations on the structure and stability of TRF1, all-atom molecular dynamics (MD) simulations on TRF1-Wild type (WT), L79R and P150R mutants for 200 ns were carried out. A significant conformational change in the structure of the P150R mutant was observed. Our integrated computational study provides a comprehensive understanding of structural changes in TRF1 incurred due to the mutations and subsequent function, leading to the progression of many diseases.Communicated by Ramaswamy H. Sarma.

ABBV-744 as a potential inhibitor of SARS-CoV-2 main protease enzyme against COVID-19

A new pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide and become pandemic with thousands new deaths and infected cases globally. To address coronavirus disease (COVID-19), currently no effective drug or vaccine is available. This necessity motivated us to explore potential lead compounds by considering drug repurposing approach targeting main protease (M^pro) enzyme of SARS-CoV-2. This enzyme considered to be an attractive drug target as it contributes significantly in mediating viral replication and transcription. Herein, comprehensive computational investigations were performed to identify potential inhibitors of SARS-CoV-2 M^pro enzyme. The structure-based pharmacophore modeling was developed based on the co-crystallized structure of the enzyme with its biological active inhibitor. The generated hypotheses were applied for virtual screening based PhaseScore. Docking based virtual screening workflow was used to generate hit compounds using HTVS, SP and XP based Glide GScore. The pharmacological and physicochemical properties of the selected lead compounds were characterized using ADMET. Molecular dynamics simulations were performed to explore the binding affinities of the considered lead compounds. Binding energies revealed that compound ABBV-744 binds to the M^pro with strong affinity (ΔG_bind -45.43 kcal/mol), and the complex is more stable in comparison with other protein-ligand complexes. Our study classified three best compounds which could be considered as promising inhibitors against main protease SARS-CoV-2 virus.

Identification of Potential Inhibitors of Calcium/Calmodulin-Dependent Protein Kinase IV from Bioactive Phytoconstituents

Calcium/calmodulin-dependent protein kinase IV (CaMKIV) is an upstream regulator of CaMKK-CaMKIV signaling cascade that activates various transcription factors, thereby regulating several cellular activities including, neuronal communication and immune response. Owing to the abnormal expression in cancer and neurodegenerative diseases, the CaMKIV has been considered a potential drug target. In the present study, we checked the binding affinity of plant-derived natural compounds viz., quercetin, ellagic acid (EA), simvastatin, capsaicin, ursolic acid, DL-α-tocopherol acetate, and limonin towards CaMKIV. Molecular docking and fluorescence binding studies showed that EA and quercetin bind to the CaMKIV with a considerable affinity in comparison to other compounds. Enzyme inhibition assay revealed that both EA and quercetin inhibit CaMKIV activity with their IC₅₀ values in the micromolar range. To get atomistic insights into the mode of interactions, inhibition mechanism, and the stability of the CaMKIV-ligand complex, a 100 ns MD simulation analysis was performed. Both EA and quercetin bind to the catalytically important residues of active site pocket of CaMKIV forming enough stabilizing interactions presumably inhibiting enzyme activity. Moreover, no significant structural change in the CaMKIV was observed upon binding of EA and quercetin. In conclusion, this study illustrates the application of phytoconstituents in the development of therapeutic molecules targeting CaMKIV having implications in cancer and neurodegenerative diseases after in vivo validation.

Molecular Assembly of Surfactant Mixtures in Oil-Swollen Micelles: Implications for High Salinity Colloidal Stability

Alkylbenzene sulfonates are one of the most important synthetic surfactant families, considering their wide applicability, cost-effectiveness, and overall consumption levels. Nevertheless, their low salt tolerance (especially divalent ion contents) prevented their wider applications such as enhanced oil recovery in high salinity reservoirs. Here, using experiments and atomistic molecular dynamics simulations, we demonstrated that the high salinity colloidal stability of alkylbenzene sulfonates can be dramatically increased by mixing with zwitterionic cosurfactants in oil-swollen micelles. By mixing with cosurfactants we had two important observations. (1) The polydispersity of surfactant mixture oil-swollen micelles were largely decreased due to the less rigid oil/water interfaces with mixed surfactants, which formed fewer but larger uniform micelles. (2) Strong dehydration of sulfonates due to the shielding from protruding more extended zwitterionic cosurfactants at the oil/water interfaces. Both observed molecular assembly characteristics triggered by the cosurfactants effectively reduced the total exposures of sulfonates to water phase that may form divalent ion bridging and large aggregates, and thus increased their high salinity colloidal stability. Lastly, it was observed that the dehydration of sulfonates was the highest at flat oil/water interfaces (very large oil-swollen micelles), which justified that adding trace amount of mineral oils may boost the high salinity colloidal stability even further.

In silico assessment of human Calprotectin subunits (S100A8/A9) in presence of sodium and calcium ions using Molecular Dynamics simulation approach

Calprotectin is a heterodimeric protein complex which consists of two subunits including S100A8 and S100A9. This protein has a major role in different inflammatory disease and various types of cancers. In current study we aimed to evaluate the structural and thermodynamic changes of the subunits and the complex in presence of sodium and calcium ions using molecular dynamics (MD) simulation. Therefore, the residue interaction network (RIN) was visualized in Cytoscape program. In next step, to measure the binding free energy, the potential of mean force (PMF) method was performed. Finally, the molecular mechanics Poisson-Boltzmann surface area (MMPBSA) method was applied as an effective tool to calculate the molecular model affinities. The MD simulation results of the subunits represented their structural changes in presence of Ca2+. Moreover, the RIN and Hydrogen bond analysis demonstrated that cluster interactions between Calprotectin subunits in presence of Ca2+ were greater in comparison with Na+. Our findings indicated that the binding free energy of the subunits in presence of Ca2+ was significantly greater than Na+. The results revealed that Ca2+ has the ability to induce structural changes in subunits in comparison with Na+ which lead to create stronger interactions between. Hence, studying the physical characteristics of the human proteins could be considered as a powerful tool in theranostics and drug design purposes.

Water Solubility and Surface Property of Alkyl Di-/Tri-/Tetraoxyethyl β-d-Xylopyranosides

Alkyl di-/tri-/tetraoxyethyl β-d-xylopyranosides as derivatives of alkyl xylosides are a class of non-ionic sugar-based surfactants. They were stereoselectively synthesized by the Helferich method. Their properties including hydrophilic-lipophilic balance number, water solubility, surface property, foam property, emulsifying property, and thermotropic liquid crystal property were mainly investigated. The results showed that their water solubility decreased with increasing the alkyl chain length and increasing the number of the oligooxyethyl fragment. The critical micelle concentration had a monotonous decreasing trend with increasing the alkyl chain length. Nonyl di-/tri-/tetraoxyethyl β-d-xylopyranosides [-(OCH₂CH₂)_m-, where m = 2, 3, and 4] exhibited the most excellent foaming ability and foam stability. In the n-octane/water system, dodecyl tetraoxyethyl β-d-xylopyranosides and tetradecyl tetraoxyethyl β-d-xylopyranosides had the strongest emulsion ability. In addition, some alkyl di-/tri-/tetraoxyethyl β-d-xylopyranosides had thermotropic liquid crystal properties. Such sugar-based surfactants, alkyl di-/tri-/tetraoxyethyl β-d-xylopyranosides, will be expected to develop for a variety of practical application.