Comparative molecular dynamic simulation study on the use of chitosan for temperature stabilization of interferon αII

Exploring the Antarctic aminopeptidase P from Pseudomonas sp. strain AMS3 through structural analysis and molecular dynamics simulation

Aminopeptidase P (APPro) is a crucial metalloaminopeptidase involved in amino acid cleavage from peptide N-termini, playing essential roles as versatile biocatalysts with applications ranging from pharmaceuticals to industrial processes. Despite acknowledging its potential for catalysis in lower temperatures, detailed molecular basis and biotechnological implications in cold environments are yet to be explored. Therefore, this research aims to investigate the molecular mechanisms underlying the cold-adapted characteristics of APPro from Pseudomonas sp. strain AMS3 (AMS3-APPro) through a detailed analysis of its structure and dynamics. In this study, structure analysis and molecular dynamics (MD) simulation of a predicted model of AMS3-APPro has been performed at different temperatures to assess structural flexibility and thermostability across a temperature range of 0-60 °C over 100 ns. The MD simulation results revealed that the structure were able to remain stable at low temperatures. Increased temperatures present a potential threat to the overall stability of AMS3-APPro by disrupting the intricate hydrogen bond networks crucial for maintaining structural integrity, thereby increasing the likelihood of protein unfolding. While the metal binding site at the catalytic core exhibits resilience at higher temperatures, highlighting its local structural integrity, the overall enzyme structure undergoes fluctuations and potential denaturation. This extensive structural instability surpasses the localized stability observed at the metal binding site. Consequently, these assessments offer in-depth understanding of the cold-adapted characteristics of AMS3-APPro, highlighting its capability to uphold its native conformation and stability in low-temperature environments. In summary, this research provides valuable insights into the cold-adapted features of AMS3-APPro, suggesting its efficient operation in low thermal conditions, particularly relevant for potential biotechnological applications in cold environments.Communicated by Ramaswamy H. Sarma.

Theoretical investigation of electronic, energetic, and mechanical properties of polyvinyl alcohol/cellulose composite hydrogel electrolyte

Hydrogels are a new class of electrolytic materials employed in zinc-air batteries due to their significant on the battery's performance. However, the effectiveness of electrolytic hydrogel is affected by factors such as water content, temperature, additives, etc. Using DMol3 and molecular dynamics modeling techniques, this research aimed at investigating the electronic properties, effect of water content, and temperature on the binding energy, cohesive energy, and the mechanical properties of polyvinyl alcohol/cellulose-based composite hydrogel at the molecular level. The electronic optimized structures of the polymeric materials and parameters such as frontier molecular orbitals, band gap and electron density were analyzed. The results revealed that the binding energies of hydrogel polymer composite increased as the number of water molecules in the composite increased up to 60 % after which the binding energy decreased. In addition, the temperature increase led to a decrease in the binding energy of the composite. The cohesive energy density of the composite was highest at 40 % water content while higher temperatures decreased the cohesive energy density of the hydrogel. As the number of water molecules increased from 29 to 256, the tensile modulus increased from 0.707 × 10-3 to 2.821 × 10-3 Gpa; while the bulk modulus (K) increased in the order of K 40 > 50 > 30 > 20 > 10 respectively. These results serve as a theoretical enlightenment and a guide for experimental works in the field of energy conversion and storage devices.

Molecular Dynamics Simulations for Rationalizing Polymer Bioconjugation Strategies: Challenges, Recent Developments, and Future Opportunities

The covalent modification of proteins with polymers is a well-established method for improving the pharmacokinetic properties of therapeutically valuable biologics. The conjugated polymer chains of the resulting hybrid represent highly flexible macromolecular structures. As the dynamics of such systems remain rather elusive for established experimental techniques from the field of protein structure elucidation, molecular dynamics simulations have proven as a valuable tool for studying such conjugates at an atomistic level, thereby complementing experimental studies. With a focus on new developments, this review aims to provide researchers from the polymer bioconjugation field with a concise and up to date overview of such approaches. After introducing basic principles of molecular dynamics simulations, as well as methods for and potential pitfalls in modeling bioconjugates, the review illustrates how these computational techniques have contributed to the understanding of bioconjugates and bioconjugation strategies in the recent past and how they may lead to a more rational design of novel bioconjugates in the future.

Repurposing FDA-approved drugs cetilistat, abiraterone, diiodohydroxyquinoline, bexarotene, and remdesivir as potential inhibitors against RNA dependent RNA polymerase of SARS-CoV-2: A comparative in silico perspective

Vaccines are undoubtedly the most effective means of combating viral diseases like COVID-19. However, there are risks associated with vaccination, such as incomplete viral deactivation or potential adverse effects in humans. However, designing and developing a panel of new drug molecules is always encouraged. In an emergency, drug repurposing research is one of the most potent and rapid options. RdRp (RNA-dependent RNA polymerase) has been discovered to play a pivotal role in viral replication. In this study, FDA-approved drugs bexarotene, diiodohydroxyquinoline, abiraterone, cetilistat, and remdesivir were repurposed against the RdRp by molecular modeling, docking, and dynamic simulation. Furthermore, to validate the potency of these drugs, we compared them to the antiviral remdesivir, which inhibits RdRp. Our finding indicated that the selected drugs have a high potential to be developed as RdRp inhibitors and, with further validation studies, could serve as potential drugs for the treatment of COVID-19.

Thermodynamic stability, in-vitro permeability, and in-silico molecular modeling of the optimal Elaeis guineensis leaves extract water-in-oil nanoemulsion

Nanoemulsion is a delivery system used to enhance bioavailability of plant-based compounds across the stratum corneum. Elaeis guineensis leaves are rich source of polyphenolic antioxidants, viz. gallic acid and catechin. The optimal E. guineensis leaves extract water-in-oil nanoemulsion was stable against coalescence, but it was under significant influence of Ostwald ripening over 90 days at 25 °C. The in-vitro permeability revealed a controlled and sustained release of the total phenolic compounds (TPC) of EgLE with a cumulative amount of 1935.0 ± 45.7 µgcm-2 after 8 h. The steady-state flux and permeation coefficient values were 241.9 ± 5.7 µgcm-2 h-1 and 1.15 ± 0.03 cm.h-1, respectively. The kinetic release mechanism for TPC of EgLE was best described by the Korsmeyer-Peppas model due to the highest linearity of R2 = 0.9961, indicating super case II transport mechanism. The in-silico molecular modelling predicted that the aquaporin-3 protein in the stratum corneum bonded preferably to catechin over gallic acid through hydrogen bonds due to the lowest binding energies of - 57.514 kcal/mol and - 8.553 kcal/mol, respectively. Thus, the in-silico study further verified that catechin could improve skin hydration. Therefore, the optimal nanoemulsion could be used topically as moisturizer to enhance skin hydration based on the in-silico prediction.

In silico investigation on the inhibitory effect of fungal secondary metabolites on RNA dependent RNA polymerase of SARS-CoV-II: A docking and molecular dynamic simulation study

The newly emerged Coronavirus Disease 2019 (COVID-19) rapidly outspread worldwide and now is one of the biggest infectious pandemics in human society. In this study, the inhibitory potential of 99 secondary metabolites obtained from endophytic fungi was investigated against the new coronavirus RNA-dependent RNA polymerase (RdRp) using computational methods. A sequence of blind and targeted molecular dockings was performed to predict the more potent compounds on the viral enzyme. In the next step, the five selected compounds were further evaluated by molecular dynamics (MD) simulation. Moreover, the pharmacokinetics of the metabolites was assessed using SwissADME server. The results of molecular docking showed that compounds 18-methoxy cytochalasin J, (22E,24R)-stigmasta-5,7,22-trien-3-β-ol, beauvericin, dankasterone B, and pyrrocidine A had higher binding energy than others. The findings of MD and SwissADME demonstrated that two fungal metabolites, 18-methoxy cytochalasin J and pyrrocidine A had better results than others in terms of protein instability, strong complex formation, and pharmacokinetic properties. In conclusion, it is recommended to further evaluate the compounds 18-methoxy cytochalasin J and pyrrocidine A in the laboratory as good candidates for inhibiting COVID-19.

A molecular dynamics study on using of naturally occurring polymers for structural stabilization of erythropoietin at high temperature

Today the nano drug delivery systems are among the hot topics in drug design and pharmacy studies. Extensive researches are conducted worldwide for obtaining more effective therapeutics and screen the best drug carrier in-vivo and in-vitro. Considering the high cost of such experiments and the ethical issues linked with in-vivo studies, the in-silico analysis provides the time and cost-effective opportunity to evaluation of physiochemical properties and the interactions between drugs and their carriers. In this study using molecular dynamics (MD) simulation, five commonly used biodegradable biopolymers in pharmaceutical formulations including Chitosan, Alginate, Cyclodextrin, Hyaluronic Acid, and Pectin were investigated as proper carriers for the erythropoietin (EPO) in heat stress. The EPO was simulated in different temperatures of 298 and 343 K and the ability of polymers for temperature stabilization of the protein was evaluated comparatively. Overall, the results obtained in this study suggest that the pectin polysaccharide is the preferable carrier than others in term of protein stability in high temperatures and using for the delivery of erythropoietin.Communicated by Ramaswamy H. Sarma.

Leflunomide Loaded Chitosan Nanoparticles for the Preparation of Aliphatic Polyester Based Skin Patches

In the present study, the preparation of controlled-released leflunomide (LFD)-loaded skin patches was evaluated, utilizing the combination of chitosan (CS) nanoparticles (NPs) incorporated into suitable poly(l-lactic acid) (PLLA) or poly(lactic-co-glycolic acid) (PLGA) polyester matrices. Initially, LFD-loaded CS NPs of ~600 nm and a smooth surface were prepared, while strong inter-molecular interactions between the drug and the CS were unraveled. In the following step, the prepared LFD-loaded CS NPs were incorporated into PLLA or PLGA, and thin-film patches were prepared via spin-coating. Analysis of the prepared films showed that the incorporation of the drug-loaded CS NPs resulted in a significant increase in the drug’s release rate and extent as compared to neat LFD-loaded polyester patches (i.e., prepared without the use of CS NPs). In-depth analysis of the prepared formulations showed that the amorphization of the drug within the matrix and the increased wetting properties of the prepared CS NPs were responsible for the improved thin-film patch characteristics.

Chitosan/tripolyphosphate nanoparticles in active and passive microchannels

BACKGROUND AND PURPOSE

In recent years, the interest in chitosan nanoparticles has increased due to their application, especially in drug delivery. The main aim of this work was to find a suitable method for simulating pharmaceutical nanoparticles with computational fluid dynamics (CFD) modeling and use it for understanding the process of nanoparticle formation in different types of microchannels.

EXPERIMENTAL APPROACH

Active and passive microchannels were compared to find the advantages and disadvantages of each system. Twenty-eight experiments were done on microchannels to quantify the effect of 4 parameters and their interactions on the size and polydispersity index (PDI) of nanoparticles. CFD was implemented by coupling reactive kinetics and the population balance method to simulate the synthesis of chitosan/tripolyphosphate nanoparticles in the microchannel.

FINDINGS/RESULTS

The passive microchannel had the best performance for nanoparticle production. The most uniform microspheres and the narrowest standard deviation (124.3 nm, PDI = 0.112) were achieved using passive microchannel. Compared to the active microchannel, the size and PDI of the nanoparticles were 28.7% and 70.5% higher for active microchannels, and 55.43% and 105.3% higher for simple microchannels, respectively. Experimental results confirmed the validity of CFD modeling. The growth and nucleation rates were determined using the reaction equation of chitosan and tripolyphosphate.

CONCLUSION AND IMPLICATIONS

CFD modeling by the proposed method can play an important role in the prediction of the size and PDI of chitosan/tripolyphosphate nanoparticles in the same condition and provide a new perspective for studying the production of nanoparticles by numerical methods.

Insight into the Microcosm of the Human Growth Hormone and Its Interactions with Polymers and Copolymers: A Molecular Dynamics Perspective

Therapeutic proteins nowadays have increasingly been applied for their considerable potential in treating a wide variety of diseases. The effectiveness and potency of native therapeutic proteins are limited by various factors (e.g., stability, blood circulation time, specificity). Over the past years, a great deal of effort has been devoted to developing safe and efficient protein delivery systems. Entrapment of protein into polymeric and copolymeric matrices is common among the different types of protein-based drug formulation. However, despite the massive efforts toward developing therapeutic protein delivery in experimental studies and industrial applications, there is relatively little data on the influence of polymers and copolymers on therapeutic proteins at the atomic and molecular levels. Herein, molecular dynamics (MD) simulations are used to study the effects of biocompatible synthetic polymers including methoxy poly(ethylene glycol) (MPEG), poly(lactic acid) (PLA), and poly(lactic acid) copolymers (poly(lactic-co-glycolic acid)) PLGA and MPEG-PLA(PELA)) on the structure and dynamics of the human growth hormone (hGH), and the results are compared with previous experimental findings. Our results indicate that the hGH conformation remains stable both in pure water and in the presence of polymers, and these results are in good agreement with previous experimental data. It is shown that the MPEG chains are self-assembled and folded into a semicrystalline structure; therefore, only a small portion of the protein interacts with the polymer. The other three polymers, however, interact well with the protein and partially cover its surface. Our findings suggest that the use of these polymers for protein encapsulation has the advantage of reducing protein aggregation and thus increasing drug serum half-life. Eventually, we anticipate that the research results will expand the current knowledge about encapsulation mechanisms and the molecular interactions between hGH and the polymers.

Interactions and effects of food additive dye Allura red on pepsin structure and protease activity; experimental and computational supports

Background and purpose:

Today, color additives such as Allura red (AR) are widely used in different kinds of food products. Pepsin is a globular protein that is secreted as a digestive protease from the main cells in the stomach. Because of the important role of pepsin in protein digestion and because of its importance in digestive diseases the study of the interactions of pepsin with chemical food additives is important.

Experimental approach:

In this study, the interactions between AR and pepsin were investigated by different computational and experimental approaches such as ultraviolet and fluorescence spectroscopy along with computational molecular modeling.

Findings/Results:

The experimental results of fluorescence indicated that AR can strongly quench the fluorescence of pepsin through a static quenching. Thermodynamic analysis of the binding phenomena suggests that van der Waals forces and hydrogen bonding played a major role in the complex formation. The results of synchronous fluorescence spectra and furrier transformed infra-red (FTIR) experiments showed that there are no significant structural changes in the protein conformation. Also, examined pepsin protease activity revealed that the activity of pepsin was increased upon ligand binding. In agreement with the experimental results, the computational results showed that hydrogen bonding and van der Waals interactions occurred between AR and binding sites.

Conclusion and implications:

From the pharmaceutical point of view, this interaction can help us to get a deeper understanding of the effect of this synthetic dye on food digestion.

A study on the protease activity and structure of pepsin in the presence of atenolol and diltiazem

Pepsin, as the main protease of the stomach, plays an important role in the digestion of food proteins into smaller peptides and performs about 20% of the digestive function. The role of pepsin in the development of gastrointestinal ulcers has also been studied for many years. Edible drugs that enter the body through the gastrointestinal tract will interact with this enzyme as one of the first targets. Continuous and long-term usage of some drugs will cause chronic contact of the drug with this protein, and as a result, the structure and function of pepsin may be affected. Therefore, the possible effect of atenolol and diltiazem on the structure and activity of pepsin was studied. The interaction of drugs with pepsin was evaluated using various experimental methods including UV-Visible spectroscopy, fluorescence spectroscopy, FTIR and enzymatic activity along with computational approaches. It was showed that after binding of atenolol and diltiazem to pepsin, the inherent fluorescence of the protein is quenched. Determination of the thermodynamic parameters of interactions between atenolol and diltiazem with pepsin indicates that the major forces in the formation of the protein-drug complexes are hydrophobic forces and also atenolol has a stronger protein bonding than diltiazem. Additional tests also show that the protease activity of pepsin, decreases and increases in the presence of atenolol and diltiazem, respectively. Investigation of the FTIR spectrum of the protein in the presence and absence of atenolol and diltiazem show that in the presence of atenolol the structure of protein has slightly changed. Molecular modeling studies, in agreement with the experimental results, confirm the binding of atenolol and diltiazem to the enzyme pepsin and show that the drugs are bind close to the active site of the enzyme. Finally, from experimental and computational results, it can be concluded that atenolol and diltiazem interact with the pepsin and change its structure and protease activity.

Cholesterol-lowering drugs the simvastatin and atorvastatin change the protease activity of pepsin: An experimental and computational study

In this study, the effect of long-term use drugs of cholesterol-lowering atorvastatin and simvastatin on the activity and molecular structure of pepsin as important gastric enzyme was investigated by various experimental and computational methods. Based on the results obtained from fluorescence experiments, both drugs can bond to pepsin and quench the fluorescence intensity of protein through the static quenching mechanism. Also analysis of the thermodynamic parameters of binding the drugs to pepsin showed that the main forces in the complex formation for both are hydrophobic interactions and van der Waals forces. The effects of the drugs on the enzymatic activity of pepsin were then investigated and results showed that in the presence of both drugs the catalytic activity of the enzyme was significantly increased in lower (0.3-0.6 mM) concentrations however about the atorvastatin, increasing the concentration (0.9 mM) decreased the protease activity of pepsin. Also as a result of the FTIR studies, it was found that binding of the drugs to protein did not significant alteration in the structure of the protein. In order to obtain the atomic details of drug-protein interactions, the computational calculations were performed. The results in good agreement with those obtained from the experimental for interaction; confirm that the drugs both are bind to a cleft near the active site of the protein without any change in the structure of pepsin. Overall from the results obtained in this study, it can be concluded that both simvastatin and atorvastatin can strongly bond to a location close to the active site of pepsin and the binding change the enzymatic activity of protein.

Physiological changes in the albumin-bound non-esterified free fatty acids critically influence heme/bilirubin binding properties of the protein: A comparative, in vitro, spectroscopic study using the endogenous biomolecules

Heme and bilirubin (BR), as by-products of red blood cells (and hemoglobin) degradation, show increased plasma concentrations in some diseases. These two toxic hydrophobic molecules are mainly transported in the blood-stream by human serum albumin (HSA) that carries a wide variety of ligands. Under normal physiological conditions, ~3 fatty acid (FA) molecules are bound to each HSA; and its possible effect on BR/heme binding remains to be more clarified. In the present study, to provide deeper insight on this issue, we purified albumin from healthy individuals (as purified non-defatted albumin or PA) with normal plasma levels of FA, then defatted some of the purified protein (as defatted-HSA; or DA). In the next step, using various spectroscopic methods, their interactions with heme and BR were investigated. By 1: 1 binding of the ligands, quenching and thermodynamic analysis of parameters indicated that binding constants (K_b) values of bilirubin and heme for PA and DA are different. It could be perceived that the presence of FAs in high-affinity FA binding sites (FABSs) exerted considerable conformational changes in the structure followed by an improved BR binding while hindered heme interaction. The data was confirmed by determining surface hydrophobicity of the purified albumin (PA) and DA, and then supported by bioinformatics analyses. The physiological and clinical relevance of the observed dynamic interactions is also discussed. This study, also, re-confirmed that the primary BR binding site is subdomain IIA not subdomain IB.

Computational investigation on the effects of pharmaceutical polymers on the structure and dynamics of interleukin2 in heat stress

Application of proteinous drugs can be associated with difficulties during both in storage/transportation and in the body when they are used. However, using pharmaceutical carbohydrates that are widely employed in drug delivery systems, besides the drug can be protected, these systems leading to gradually release the drug over time, or deliver it to the target cell. Using a combination of molecular modeling and simulation techniques, in this study the effects of five carbohydrate polymers of Chitosan, Alginate, Cyclodextrin, Hyaluronic acid and Pectin on structure and dynamics of interleukin2 protein at 298 K and 343 K, are investigated. Data achieved using molecular modeling methods showed that when the temperature rises, the protein stability decreases. Among different polymers, Chitosan and Cyclodextrin have shown to be able to protect protein against the negative effects of high temperatures in comparison with other polymers which suggests that the use of Cyclodextrin biopolymer for the preparation of pharmaceutical formulations of interleukin2 can be the best possible choice among other polymers investigated in this research.Communicated by Ramaswamy H. Sarma.

Multi spectroscopy and molecular modeling aspects related to drug interaction of aspirin and warfarin with pepsin; structural change and protease activity

This study evaluates the biochemical interactions between two widely used anticoagulants agents, Aspirin and Warfarin, with the Pepsin as the main stomach protease. These two drugs usually prescribe orally for long period daily use to reduce cardiovascular and thrombi death which leads to being in close contact with Pepsin. This interaction could induce related gastrointestinal problems such as peptic ulcer. In this regard, the conformational changes and enzymatic activity of the Pepsin induced by Aspirin and Warfarin were studied by using several spectroscopic methods along with molecular modeling approaches. Results confirm the formation of stable complexes between protein and drugs which leads to slight subsequent conformational changes of protein structure. The quenching mechanisms for both drug-Pepsin interactions are static. In the case of Warfarin, the hydrophobic interactions are the most important interactions. Also for Aspirin, hydrogen bond and van der Waals forces are mainly involved in the binding process. The Warfarin shows the induction of some conformational changes resulted in suppressing the protease activity and the Aspirin reversely enhanced the enzyme activity function. This study provides useful information regarding the effects of Warfarin and Aspirin on Pepsin which are helpful for the choosing of therapeutics depending on the patients' condition.

TSGA10 overexpression inhibits angiogenesis of HUVECs: A HIF-2α biased perspective

Testis-specific gene antigen 10 (TSGA10) is a protein overexpressed in most cancers; except for some certain types where its expression is reduced. TSGA10 overexpression in HeLa cells has been shown to disrupt hypoxia inducible factor-1α (HIF-1α) axis and exert potent inhibitory effects. Since HIF-1α is structurally and biochemically similar to HIF-2α, TSGA10 is expected to bind HIF-2α and inhibit its function as well. This study elucidated that increased expression of TSGA10 in manipulated human umbilical vein endothelial cells (HUVECs) decreased the proliferation and migration of these cells as affirmed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and wound healing tests, respectively. It also inhibited in vitro angiogenesis of these cells in 3D collagen-cytodex model. Expression levels of genes controlled by HIF-2α including autocrine vascular endothelial growth factor (VEGF) were also assessed using real-time PCR. Our bioinformatic analysis also showed that TSGA10 could bind HIF-2α. Moreover, flow cytometry results indicated a cell cycle arrest in G2/M. Therefore, this study showed that overexpression of TSGA10, as a tumor suppressor gene, in endothelial cells resulted in decreased proliferation, migration and therefore, angiogenic activity of HUVECs. Since angiogenesis is vital for tumor development and metastasis, our findings could be of clinical significance in cancer therapy.

Pharmaceutical applications of chitosan

Chitosan (CS) is a linear polysaccharide which is achieved by deacetylation of chitin, which is the second most plentiful compound in nature, after cellulose. It is a linear copolymer of β-(1 → 4)-linked 2-acetamido-2-deoxy-β-d-glucopyranose and 2-amino-2-deoxy-β-d-glucopyranose. It has appreciated properties such as biocompatibility, biodegradability, hydrophilicity, nontoxicity, high bioavailability, simplicity of modification, favorable permselectivity of water, outstanding chemical resistance, capability to form films, gels, nanoparticles, microparticles and beads as well as affinity to metals, proteins and dyes. Also, the biodegradable CS is broken down in the human body to safe compounds (amino sugars) which are easily absorbed. At present, CS and its derivatives are broadly investigated in numerous pharmaceutical and medical applications including drug/gene delivery, wound dressings, implants, contact lenses, tissue engineering and cell encapsulation. Besides, CS has several OH and NH₂ functional groups which allow protein binding. CS with a deacetylation degree of ~50% is soluble in aqueous acidic environment. While CS is dissolved in acidic medium, its amino groups in the polymeric chains are protonated and it becomes cationic which allows its strong interaction with different kinds of molecules. It is believed that this positive charge is responsible for the antimicrobial activity of CS through the interaction with the negatively charged cell membranes of microorganisms. This review presents properties and numerous applications of chitosan-based compounds in drug delivery, gene delivery, cell encapsulation, protein binding, tissue engineering, preparation of implants and contact lenses, wound healing, bioimaging, antimicrobial food additives, antibacterial food packaging materials and antibacterial textiles. Moreover, some recent molecular dynamics simulations accomplished on the pharmaceutical applications of chitosan were presented.