From Linear to Nets: Multiconfiguration Polymer Structure Generation with PolyFlin.

Molecular modeling and simulations are essential tools in polymer science and engineering, enabling researchers to predict and understand the properties of macromolecules, including their structure, dynamics, thermodynamics, and overall material characteristics. However, one of the key challenges in polymer simulation and modeling lies in the initial topology design, as existing programs often lack the capability to generate all types of polymer forms. In this study, we present PolyFlin, a powerful Python module that addresses this limitation by allowing the generation of a wide range of polymer structures, from simple homopolymers to complex copolymers, including grafts, cyclic, star, dendrimers, and nets. PolyFlin offers a versatile and efficient tool for exploring and creating diverse polymer architectures, facilitating advancements in various fields that require precise polymer modeling and simulation.

Revelation of potential drug targets of luteolin in Plasmodium falciparum through multi-target molecular dynamics simulation studies.

In-silico techniques offer a fast, accurate, reliable, and economical approach to studying the molecular interactions between compounds and proteins. In this study, our main aim is to use in-silico techniques as a rational approach for the prediction of the molecular drug targets for luteolin against Plasmodium falciparum. Multi-target molecular docking, 100 nanoseconds (ns) molecular dynamics (MD) simulations, and Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) binding free energy calculations were carried out for luteolin against dihydrofolate reductase thymidylate synthase (PfDHFR-TS), dihydroorotate dehydrogenase (PfDHODH), and falcipain-2. The native ligands of each protein were used as a reference to evaluate the performance of luteolin. Luteolin outperformed the native ligands of all proteins at molecular docking and MD simulations studies. However, in the MM-GBSA calculations, luteolin outperformed the native ligand of only PfDHFR-TS but not PfDHODH and falcipain-2. Among the studied proteins, the in-silico approach predicted PfDHFR-TS as the most favorable drug target for luteolin.Communicated by Ramaswamy H. Sarma.

In-silico screening of Acacia pennata and Bridelia retusa reveals pinocembrin-7-O-ß-D-glucopyranoside as a promising ß-lactamase inhibitor to combat antibiotic resistance.

The ß-lactamase of Pseudomonas aeruginosa is known to degrade ß-lactam antibiotics such as penicillins, cephalosporins, monobactams, and carbapenems. With the discovery of an extended-spectrum ß-lactamase in a clinical isolate of P. aeruginosa, the bacterium has become multi-drug resistant. In this study, we aim to identify new ß-lactamase inhibitors by virtually screening a total of 43 phytocompounds from two Indian medicinal plants. In the molecular docking studies, pinocembrin-7-O-ß-D-glucopyranoside (P7G) (-9.6 kcal/mol) from Acacia pennata and ellagic acid (EA) (-9.2 kcal/mol) from Bridelia retusa had lower binding energy than moxalactam (-8.4 kcal/mol). P7G and EA formed 5 (Ser62, Asn125, Asn163, Thr209, and Ser230) and 4 (Lys65, Ser123, Asn125, and Glu159) conventional hydrogens bonds with the active site residues. 100 ns MD simulations revealed that moxalactam and P7G (but not EA) were able to form a stable complex. The binding free energy calculations further revealed that P7G (-59.6526 kcal/mol) formed the most stable complex with ß-lactamase when compared to moxalactam (-46.5669 kcal/mol) and EA (-28.4505 kcal/mol). The HOMO-LUMO and other DFT parameters support the stability and chemical reactivity of P7G at the active site of ß-lactamase. P7G passed all the toxicity tests and bioavailability tests indicating that it possesses drug-likeness. Among the studied compounds, we identified P7G of A. pennata as the most promising phytocompound to combat antibiotic resistance by potentially inhibiting the ß-lactamase of P. aeruginosa.Communicated by Ramaswamy H. Sarma.

Stem Cell's Secretome Delivery Systems.

Stem cells' secretome contains biomolecules that are ready to give therapeutic activities. However, the biomolecules should not be administered directly because of their in vivo instability. They can be degraded by enzymes or seep into other tissues. There have been some advancements in localized and stabilized secretome delivery systems, which have increased their effectiveness. Fibrous, in situ, or viscoelastic hydrogel, sponge-scaffold, bead powder/ suspension, and bio-mimetic coating can maintain secretome retention in the target tissue and prolong the therapy by sustained release. Porosity, young's modulus, surface charge, interfacial interaction, particle size, adhesiveness, water absorption ability, in situ gel/film, and viscoelasticity of the preparation significantly affect the quality, quantity, and efficacy of the secretome. Therefore, the dosage forms, base materials, and characteristics of each system need to be examined to develop a more optimal secretome delivery system. This article discusses the clinical obstacles and potential solutions for secretome delivery, characterization of delivery systems, and devices used or potentially used in secretome delivery for therapeutic applications. This article concludes that secretome delivery for various organ therapies necessitates the use of different delivery systems and bases. Coating, muco-, and cell-adhesive systems are required for systemic delivery and to prevent metabolism. The lyophilized form is required for inhalational delivery, and the lipophilic system can deliver secretomes across the blood-brain barrier. Nano-sized encapsulation and surface-modified systems can deliver secretome to the liver and kidney. These dosage forms can be administered using devices such as a sprayer, eye drop, inhaler, syringe, and implant to improve their efficacy through dosing, direct delivery to target tissues, preserving stability and sterility, and reducing the immune response.

Multi-target molecular dynamic simulations reveal glutathione-S-transferase as the most favorable drug target of knipholone in Plasmodium falciparum.

Knipholone is an antiplasmodial phytocompound obtained from the roots of Kniphofia foliosa. Despite several available studies, the molecular drug targets of knipholone in P. falciparum remained unknown. Nowadays, in silico techniques are widely used to study the molecular interactions between compounds and proteins as they provide results quickly with high precision and accuracy. In this study, we aim to identify the potential molecular drug targets of knipholone in P. falciparum. We selected 10 proteins of P. falciparum with unique metabolic functions and we found that knipholone showed better binding affinity than the native ligands of 6 proteins. Out of the 6 proteins, knipholone showed better enzyme inhibitory potential than the native ligands of 4 proteins. We carried out a 100 ns MD simulations for knipholone and the native ligands of four proteins and this was followed by binding free energy calculations. In each step, the performance of knipholone was compared to the native ligands of the proteins. Knipholone outperformed the native ligand of Glutathione-S-Transferase (1OKT) at crucial computational studies as evidence from the lower protein-ligand root mean square deviation value, protein root mean square fluctuation value, and protein-ligand binding free energies. The ligand properties of knipholone provide additional evidence for its stability and it maintains adequate protein-ligand contacts during the entire simulation. The density functional theory study also supported the stability of knipholone at the active binding site of 1OKT. From the studied proteins, we conclude that Glutathione-S-Transferase is the most favorable drug target for knipholone in P. falciparum.Communicated by Ramaswamy H. Sarma.

Complexed Polymer Film-Forming Spray: An Optimal Delivery System for Secretome of Mesenchymal Stem Cell as Diabetic Wound Dressing?

Diabetes-related wounds have physiological factors that make healing more complicated. High sugar levels can increase microbial infection risk while limiting nutrition and oxygen transfer to the wound area. The secretome of mesenchymal stem cells has been widely known for its efficacy in regenerative therapy. However, applying the secretome directly to the wound can reduce its effectiveness. In this review, we examined the literature on synthesizing the combinations of carboxymethyl chitosan, hyaluronic acid, and collagen tripeptides, as well as the possibility of physicochemical properties enhancement of the hydrogel matrix, which could potentially be used as an optimal delivery system of stem cell's secretome for diabetic wound healing.

Preparation of Mangosteen Peel Extract Microcapsules by Fluidized Bed Spray-Drying for Tableting: Improving the Solubility and Antioxidant Stability.

Mangosteen fruit has been widely consumed and used as a source of antioxidants, either in the form of fresh fruit or processed products. However, mangosteen peel only becomes industrial waste due to its bitter taste, low content solubility, and poor stability. Therefore, this study aimed to design mangosteen peel extract microcapsules (MPEMs) and tablets to overcome the challenges. The fluidized bed spray-drying method was used to develop MPEM, with hydroxypropyl methylcellulose (HPMC) as the core mixture and polyvinyl alcohol (PVA) as the coating agent. The obtained MPEM was spherical with a hollow surface and had a size of 411.2 µm. The flow rate and compressibility of MPEM increased significantly after granulation. A formula containing 5% w/w polyvinyl pyrrolidone K30 (PVP K30) as a binder had the best tablet characteristics, with a hardness of 87.8 ± 1.398 N, friability of 0.94%, and disintegration time of 25.75 ± 0.676 min. Microencapsulation of mangosteen peel extract maintains the stability of its compound (total phenolic and α-mangosteen) and its antioxidant activity (IC50) during the manufacturing process and a month of storage at IVB zone conditions. According to the findings, the microencapsulation is an effective technique for improving the solubility and antioxidant stability of mangosteen peel extract during manufacture and storage.

Antiviral phytocompounds "ellagic acid" and "(+)-sesamin" of Bridelia retusa identified as potential inhibitors of SARS-CoV-2 3CL pro using extensive molecular docking, molecular dynamics simulation studies, binding free energy calculations, and bioactivity prediction.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected billions and has killed millions to date. Studies are being carried out to find therapeutic molecules that can potentially inhibit the replication of SARS-CoV-2. 3-chymotrypsin-like protease (3CL pro) involved in the polyprotein cleavage process is believed to be the key target for viral replication, and hence is an attractive target for the discovery of antiviral molecules. In the present study, we aimed to identify natural phytocompounds from Bridelia retusa as potential inhibitors of SARS-CoV-2 3CL pro (PDB ID: 6M2N) using in silico techniques. Molecular docking studies conducted with three different tools in triplicates revealed that ellagic acid (BR6) and (+)-sesamin (BR13) has better binding affinity than the co-crystal inhibitor "3WL" of 6M2N. BR6 and BR13 were found to have a high LD50 value with good bioavailability. 3WL, BR6, and BR13 bind to the same active binding site and interacted with the HIS41-CYS145 catalytic dyad including other crucial amino acids. Molecular dynamics simulation studies revealed stability of protein-ligand complexes as evidenced from root-mean-square deviations, root-mean-square fluctuations (RMSF), protein secondary structure elements, ligand-RMSF, protein-ligand contacts, ligand torsions, and ligand properties. BR6 (-22.3064 kcal/mol) and BR13 (-19.1274 kcal/mol) showed a low binding free energy value. The Bayesian statistical model revealed BR6 and BR13 as better protease inhibitors than 3WL. Moreover, BR6 and BR13 had already been reported to elicit antiviral activities. Therefore, we conclude that ellagic acid and (+)-sesamin as natural antiviral phytocompounds with inhibitory potential against SARS-CoV-2 3CL pro. Supplementary information: The online version contains supplementary material available at 10.1007/s11224-022-01959-3.

Silybin phytosome attenuates cerebral ischemia-reperfusion injury in rats by suppressing oxidative stress and reducing inflammatory response: In vivo and in silico approaches.

The present study was aimed to develop silybin phytosome (SIBP) and evaluate its effectiveness against cerebral ischemia-reperfusion (CIR) injury in rats. Initially, SIBP was prepared and characterized with Fourier transform-infrared spectroscopy, differential scanning calorimetry, and scanning electron microscopy. Drug loading and entrapment efficiency of SIBP were also calculated. High-performance liquid chromatography was used to carry out bioavailability studies of SIBP. Adult Wistar rats were divided randomly into five groups. The CIR injury was induced after 14 days of pretreatment by occlusion of bilateral common carotid arteries for 30 min followed by 4 h of reperfusion. Biochemical estimation, histopathological studies, and in silico studies were carried out. Bioavailability studies revealed that SIB concentration was increased to twofolds in SIBP-treated rats. SIBP treatment significantly increases superoxide dismutase and glutathione levels while it decreases monoaldehyde, tumor necrosis factor-α (TNF-α), and interleukin 6 (IL-6) levels in both the hippocampus and cortex of the SIBP-treated CIR-injured rats. Histopathological studies reveal SIBP treatment alleviates cortex cell death and arrangement of CA1 neurons in CIR-injured rats. In silico studies against proteins (TNF-α and IL-6) involved in cerebral ischemia revealed that silybin (SIB) exhibits strong binding interaction with the target proteins when compared to thalidomide which was used as the positive control. Phytosome increase SIB bioavailability and SIBP treatment showed promising results when compared to treatment with SIB only. Based on our study, we conclude that phytosome is a suitable drug delivery agent to the brain for SIB as SIBP treatment was able to provide neuroprotective action against CIR injury.

Liposome-polymer complex for drug delivery system and vaccine stabilization.

Liposomes have been used extensively as micro- and nanocarriers for hydrophobic or hydrophilic molecules. However, conventional liposomes are biodegradable and quickly eliminated, making it difficult to be used for delivery in specific routes, such as the oral and systemic routes. One way to overcome this problem is through complexation with polymers, which is referred to as a liposome complex. The use of polymers can increase the stability of liposome with regard to pH, chemicals, enzymes, and the immune system. In some cases, specific polymers can condition the properties of liposomes to be explicitly used in drug delivery, such as targeted delivery and controlled release. These properties are influenced by the type of polymer, crosslinker, interaction, and bond in the complexation process. Therefore, it is crucial to study and review these parameters for the development of more optimal forms and properties of the liposome complex. This article discusses the use of natural and synthetic polymers, ways of interaction between polymers and liposomes (on the surface, incorporation in lamellar chains, and within liposomes), types of bonds, evaluation standards, and their effects on the stability and pharmacokinetic profile of the liposome complex, drugs, and vaccines. This article concludes that both natural and synthetic polymers can be used in modifying the structure and physicochemical properties of liposomes to specify their use in targeted delivery, controlled release, and stabilizing drugs and vaccines.

Film-Forming Spray of Water-Soluble Chitosan Containing Liposome-Coated Human Epidermal Growth Factor for Wound Healing.

Human epidermal growth factor (hEGF) has been known to have excellent wound-healing activity. However, direct application to the wound area can lead to low hEGF bioavailability due to protease enzymes or endocytosis. The use of liposomes as coatings and carriers can protect hEGF from degradation by enzymes, chemical reactions, and immune reactions. Sustained release using a matrix polymer can also keep the levels of hEGF in line with the treatment. Therefore, this study aimed to develop a film-forming spray of water-soluble chitosan (FFSWSC) containing hEGF-liposomes as a potential wound dressing. The hEGF-liposomes were prepared using the hydration film method, and the preparation of the FFSWSC was achieved by the ionic gelation method. The hydration film method produced hEGF-liposomes that were round and spread with a Z-average of 219.3 nm and encapsulation efficiency of 99.87%, whereas the film-forming solution, which provided good sprayability, had a formula containing 2% WSC and 3% propylene glycol with a viscosity, spray angle, droplet size, spray weight, and occlusion factor of 21.94 ± 0.05 mPa.s, 73.03 ± 1.28°, 54.25 ± 13.33 µm, 0.14 ± 0.00 g, and 14.57 ± 3.41%, respectively. The pH, viscosity, and particle size of the FFSWSC containing hEGF-liposomes were stable during storage for a month in a climatic chamber (40 ± 2 °C, RH 75 ± 5%). A wound healing activity test on mice revealed that hEGF-liposomes in FFSWSC accelerated wound closure significantly, with a complete wound closure on day 6. Based on the findings, we concluded that FFSWSC containing hEGF-liposomes has the potential to be used as a wound dressing.

Flavonoid compounds of buah merah (Pandanus conoideus Lamk) as a potent SARS-CoV-2 main protease inhibitor: in silico approach.

BACKGROUND: COVID19 is a global pandemic that threatens all nations. As there is no effective antiviral drug for COVID19, we examined the potency of natural ingredients against the SARS-CoV-2 main protease (PDB ID 6YNQ). Buah merah is a typical fruit from Papua, Indonesia, which is known to contain high levels of carotenoids and flavonoids. The contents have been proven to be effective as antiparasitic and anti-HIV. An in silico approach to 16 metabolites of buah merah (Pandanus conoideus Lamk) was carried out using AutoDock Vina. Furthermore, the study of the dynamics of ligand-protein interactions was carried out using CABS Flex 2.0 server to determine the test ligand and receptor complexes' stability. ADMET prediction was also carried out to study the pharmacokinetic profile of potential antiviral candidates. RESULT: The docking results showed that 3 of the 16 buah merah metabolites were potent inhibitors against the SARS-CoV-2 main protease. The flavonoid compounds are quercetin 3'-glucoside, quercetin 3-O-glucose, and taxifolin 3-O-α-arabinopyranose with a binding affinity of - 9.7, - 9.3, and - 8.8, respectively, with stable ligand-protein complex. ADMET study shows that the three compounds are easily dissolved, easily absorbed orally and topically, have a high unbound fraction, low toxicity, and non-irritant. CONCLUSION: We conclude that quercetin 3'-glucoside, quercetin 3-O-glucose, and taxifolin 3-O-α-arabinopyranose can be used and improved as potential anti-SARS-CoV-2 agents in further study.

Characterization and acute oral toxicity of concentrated minerals of Pamekasan Madura seawater.

Indonesia is a maritime country with abundant seawater mineral content. One of the regions with the highest salt production is Pamekasan Madura. Minerals are known to have many roles and benefits for our bodies, such as regulating fluid balance and metabolism. Therefore, this study aimed to characterize the physicochemical and microbial properties of concentrated minerals obtained through solvent evaporation and salt deposition for ± 60 days. Acute oral toxicity examination was performed as a first step in determining the safety of concentrated minerals to be used as a raw material for drugs. Based on the test results, the concentrated mineral has a clear yellow color, salty taste, and a bit bitter, odorless, with a pH of 6.6 ± 0.21. Concentrated minerals have high mineral content with levels of potassium, sodium, magnesium, boron, and calcium being 44734.1598 ± 12950.4633, 33192.1198 ± 2699.3419, 8738.1388 ± 100.4894, 2092.5715 ± 60.3224, and 276.9704 ± 13.1133 mg/Kg, respectively. The results of microbiological analysis of untreated concentrated minerals (without antimicrobials or sterilization) showed that the total plate count was within limits, including coliform and Salmonella. However, the total mold and yeast levels exceed the threshold. Based on the results of acute oral toxicity testing, the concentrated mineral is practically nontoxic. With high mineral content and low toxicity, it can be concluded that the concentrated minerals from Pamekasan Madura seawater is potential to be used as a raw medicinal material.

Activity and Effectiveness of Recombinant hEGF Excreted by Escherichia coli BL21 on Wound Healing in Induced Diabetic Mice.

CONTEXT: Human epidermal growth factor (hEGF) has biological activities and can be used in medicines and cosmetics. A high level of effectiveness of hEGF can be obtained when three disulfide bonds fold perfectly. Extracellular secretion from E. coli BL21 using the PelB signal peptide is a new way to obtain hEGF with a structure that folds appropriately. OBJECT: This study aimed to determine the activity and effectiveness of recombinant hEGF excreted by E. coli BL21 on wound healing in induced diabetic mice. METHODS: Cell proliferation and migration tests were performed on NIH3T3 cells, followed by wound healing tests in induced diabetic mice, along with histological and endotoxin test at various hEGF concentrations (25, 50, and 75 µg/mL). RESULTS: Based on the results, hEGF at a level of 50 µg/mL showed optimal proliferation and migration activities. Wound healing in induced diabetic mice showed faster-wound closure within 12 days at hEGF 50 and 75 µg/mL with a percentage wound closure of 95% and 98.5%, respectively, which was significant versus control. In the histology test, the number of fibroblasts showed an increase and was significant at hEGF 75 µg/mL compared to the control group. The single test vial (STV) showed that hEGF solution was free of endotoxin. CONCLUSION: Recombinant hEGF produced by extracellular secretion using E. coli BL21 has optimal diabetic wound healing activity through increased fibroblast proliferation.

Enteric-Coated Strategies in Colorectal Cancer Nanoparticle Drug Delivery System.

Colorectal cancer is one of the most common cancer diseases with the increase of cases prevalence >5% every year. Multidrug resistance mechanisms and non-localized therapy become primary problems of chemotherapy drugs for curing colorectal cancer disease. Therefore, the enteric-coated nanoparticle system has been studied and proved to be able to resolve those problems with good performance for colorectal cancer. The highlight of our review aims to summarize and discuss the enteric-coated nanoparticle drug delivery system specific for colorectal cancer disease. The main and supporting literatures were collected from published research articles of journals indexed in Scopus and PubMed databases. In the oral route of administration, Eudragit pH-sensitive copolymer as a coating agent prevents the degradation of the nanoparticle system from the gastric fluid and releases drug to intestinal-colon track. Therefore, it provides a colon-specific targeting ability. Impressively, enteric-coated nanoparticles having a sustained release profile significantly increase the cytotoxic effect of chemotherapeutic drugs and achieve cell-specific target delivery. The enteric-coated nanoparticle drug delivery system represents an excellent modification to improve the effectiveness and performance of anticancer drugs for colorectal cancer disease in terms of the oral route of administration.

Film-Forming Sprays for Topical Drug Delivery.

Film-forming sprays offer many advantages compared to conventional topical preparations because they can provide uniform drug distribution and dose, increased bioavailability, lower incidence of irritation, continuous drug release, and accelerated wound healing through moisture control. Film-forming sprays consist of polymers and excipients that improve the characteristics of preparations and enhance the stability of active substances. Each type of polymer and excipient will produce films with different features. Therefore, the various types of polymers and excipients and their evaluation standards need to be examined for the development of a more optimal form of film-forming spray. The selected literature included research on polymers as film-forming matrices and the application of these sprays for medical purposes or for potential medical use. This article discusses the types and concentrations of polymers and excipients, sprayer types, evaluations, and critical parameters in determining the sprayability and film characteristics. The review concludes that both natural and synthetic polymers that have in situ film or viscoelastic properties can be used to optimise topical drug delivery.

Stabilization of eye drops containing autologous serum and recombinant human epidermal growth factor for dry eye syndrome.

Human epidermal growth factor (hEGF) and autologous serum are considered safer and more effective in treating dry eye syndrome. However, suitable formulas and preparation methods are needed to obtain eye drop containing autologous serum and hEGF, which are stable during storage and use. Therefore, this study aimed to develop a stable and effective eye drops containing autologous serum and hEGF. Stabilization of autologous serum and hEGF was done by adding lyoprotectant and antioxidant agents, and then prepared using the freeze-drying method. The clarity, pH, sterility, and endotoxin content of the preparation were evaluated. The effectiveness of the preparation was assessed by a cell viability test using a WST-8 reagent. Based on the results, all formulas produce preparations that are isotonic, clear, sterile, stable, and free from endotoxins. Cell viability test shows the addition of 25 µg/mL hEGF increased epithelial cell proliferation by up to 197%. It can be concluded that eye drops containing autologous serum and 25 µg/mL hEGF can be a promising therapy for dry eye syndrome.