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Various components of the tobacco plant (Nicotiana tabacum L.) have undergone pharmacological assessment to highlight their traditional role in addressing different health conditions. The anti-inflammatory properties of thirteen natural substances were investigated through the use of molecular docking conducted with AutoDock 4.2.6 Tools and Molecular Dynamics Simulations (MDS) executed with GROMACS 2016.3. ADME characteristics were assessed using SwissADME (absorption, distribution, metabolism, and excretion). Chlorogenic acid and rutin, plant-derived natural compounds, showed substantial binding tendencies with cyclooxygenase-1 (COX-1), phosphodiesterase-4 (PDE4), cyclooxygenase-2 (COX-2), phosphodiesterase-7 (PDE7), interleukin-17A (IL-17A), interleukin-1 beta (IL-1β), tumor necrosis factor-alpha (TNF-α), prostaglandin E2 (PGE2), and prostaglandin F synthase. Rutin emerged as the most notable among the tested compounds (docking energy: −11.0 kcal/mol against PDE7 and prostaglandin F synthase). Chlorogenic acid also displayed substantial and noteworthy binding energies of −9.4 kcal/mol with PDE4 and PDE7 receptors. Consequently, these investigated natural compounds could potentially serve as agents that reduce inflammation and require additional in vitro and in vivo studies to aid the creation of new anti-inflammatory drugs.

Helminth infections can be effectively treated with various anthelmintics. However, the potential for drug resistance and the need for repeated doses to ensure successful treatment are some limitations to the treatment. This study aimed to evaluate the ability of phytochemicals from Syzygium aqueum to inhibit ATP-dependent 6-phosphofructokinase (6-PFK) from Ascaris lumbricoides and Ascaris suum using the in silico method (molecular docking, molecular dynamics simulation, and ADMET analysis) and in vitro evaluation using mortality, paralysis, and ovicidal activity testing. Molecular docking outcomes indicated that out of 76 compounds from Syzygium aqueum, 18 molecules exhibited strong inhibition against the target enzyme, based on binding free energy and interaction patterns. Molecular dynamics simulation demonstrated that samarangenin A and butyrospermol complexes remained stable for up to 200 ns within a range below 1 nm. The most promising compounds also exhibited good ADMET properties. In the in vitro egg hatch test, a 10% concentration of Syzygium aqueum extract showed potent ovicidal properties by significantly reducing the number of fertile eggs but was less effective than 0.12% albendazole. However, ferulic acid at various concentrations exhibited minimal effect on egg fertility but showed increased mortality and incidence of paralysis at higher doses against male worms. These findings yielded valuable insights into the underlying mechanisms, providing essential clues for the development of highly efficient inhibitors for parasitic worm infections through structure-based design.

Emerging clinical observations underscore the correlation between interleukin-8 (IL-8) and rosacea. Increased IL-8 expression has been detected in rosacea samples, particularly in moderate to severe manifestations. This phenomenon has prompted the exploration of IL-8 as a prospective therapeutic target for rosacea treatment. To this end, a selection of compounds sourced from the ZINC database, encompassing six small molecules, was made with the intent of identifying promising lead candidates that exhibit drug-like characteristics against IL-8. Through an integrated in silico approach involving structure-guided drug design, encompassing molecular docking, molecular dynamics (MD) simulation, molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analysis, protein-peptide docking, and scrutiny of toxicity profiles, it was ascertained that the small molecule ZINC000022339916 effectively inhibits IL-8 activity. These findings present a novel lead compound that warrants further validation through in vitro, in vivo, and ongoing clinical investigations to confirm its potential for therapeutic management of rosacea.

In the effort to combat SARS-CoV-2 infection, researchers are currently exploring the repurposing of conventional antiviral drugs, despite their limited efficacy. The SARS-CoV-2 virus encodes a papain-like protease (PLpro), which not only plays a crucial role in viral replication but also cleaves ubiquitin and interferon-stimulated gene 15 protein (ISG15) from host proteins, making it a prime target for the development of new antiviral medications. In this study, we conducted a multi-step in silico screening to identify novel, noncovalent PLpro inhibitors. Curcumin, an antioxidant derived from turmeric rhizomes (Curcuma longa L.), has undergone extensive preclinical investigations and shown significant efficacy against viruses and other ailments in both laboratory and animal studies. However, the pharmacological limitations of curcumin have prompted the synthesis of numerous novel curcumin analogs, necessitating evaluation for their therapeutic potential. The selectivity of the top-scoring compounds was assessed through molecular docking studies and molecular dynamics simulations to determine their binding affinity to PLpro. As a result, we identified 20 potential, selective PLpro inhibitors, from which the top two compounds (THA111 and THHGV6) were selected based on their binding free energy values towards PLpro as estimated by MM-PBSA calculations. These selected candidates demonstrate promising activity against the protein, with binding free energy values ranging from approximately −105 to −108 kJ/mol, and largely adopt a similar binding mode to known noncovalent SARS-CoV-2 PLpro inhibitors (GRL0617 = −100.98 kJ/mol). We further propose these two most promising compounds for future in vitro evaluation. The findings for the top potential PLpro inhibitors have been deposited in a database (Curcumin Research Center) to aid research on anti-SARS-CoV-2 drugs.

The human body naturally has an antioxidant system to counteract free radical reactivity in a sustainable manner, but if the number of free radicals in the body is excessive, additional antioxidants are needed from food intake, namely vitamin C, vitamin E, carotenes and flavonoids. One plant that has the potential as an antioxidant is Ziziphus spina-christi (ZSC) because it contains phenolics and flavonoids. This study aims to determine the flavonoid content both qualitatively and quantitatively and to test the antioxidant activity of ZSC leaf extract using in vitro and in silico attenuation methods. Determination of the total flavonoid content of ZSC leaf extract using a comparison of quercetin. In vitro the antioxidant activity assay of ZSC leaf extract was carried out by measuring the reducing activity of ZSC leaf extract against the radical DPPH using ascorbic acid as a comparison, while the in silico method used QSAR and pharmacophore modelling techniques. The results showed that the total flavonoid content obtained from ZSC leaf extract was 0.2515 ± 0.0013 mg QE/g D.W with an IC50 of 58.9296 ppm. Furthermore, from the in silico method using pharmacophore modeling and QSAR techniques, 8 hit compounds were obtained from the content of ZSC with IC50 QSAR ranging from 6.57 μM to 0.0004 μM, which was thought to be the metabolite that had the most role in its antioxidant activity. This value indicates that ZSC leaf extract has potential as a very strong antioxidant. ZSC leaf extract can be used as an antioxidant candidate in drug and cosmetic preparations through the oral or percutaneous route. It also proves that QSAR and pharmacophore modelling techniques can be used as confirmatory tests for in vitro results in determining the antioxidant activity of natural materials.

Coronavirus 19 (COVID-19) is still a global health issue to date, SARS-CoV-2 is a novel coronavirus that is responsible for this sickness. The receptor-binding domain of the SARS-CoV-2 virus associates with angiotensin-converting enzyme 2 (ACE-2) and allows the virus to enter human cells. Natural peptides such alpha-defensin are thought to attach to the SARS-CoV-2 RBD and prohibit it from engaging with ACE-2. Molecular dynamics simulations using a computational approach are utilized to understand the stability of six alpha-defensin macromolecules using the Gromacs 2016 software. The trajectories formed are then analyzed using VMD 1.9.4 and BIOVIA Discovery Studio 2020 software. Finally, the free energy is estimated using the MM/PBSA method. The alpha-defensins 2 macromolecules were found to have the best stability based on numerous study results (trajectory visualization, RMSD, RMSF, and free energy calculations). As a result, these macromolecules could be used to build new antiviral treatments for COVID-19 infectious disease candidates.

Citrus peels contain various phytochemical active compounds such as flavonoids that are useful for antiaging cosmetic products. This study was conducted to identify the anti-collagenase and anti-elastase activities of flavonoid compounds in citrus peel and to determine the molecular interaction mechanism using the molecular docking method. The study was carried out through several stages, including preparation of enzyme macromolecules, preparation of flavonoid compound molecules, validation of molecular docking, identification of binding-free energy, visualization of interaction conformations, and predictions of molecular skin toxicity. The result showed that the flavonoid compounds in citrus peel (hesperidin, naringin, nobiletin, and tangeretin) could bind to collagenase and elastase enzymes. Naringin has the highest affinity for the collagenase enzyme with the binding-free energy of −9.52 kcal/mol, while nobiletin has the highest affinity for the elastase enzyme with the binding-free energy of −6.44 kcal/mol. Compared to EGCG (epigallocatechin gallate), the flavonoid compounds have a lower affinity for the collagenase enzyme but a higher affinity for elastase enzymes. Hydrogen bonds and the hydrophobic interactions dominate the interaction between citrus peel’s flavonoids against the enzymes. When applied to the skin, flavonoid compounds are predicted to have no risk of skin toxicity. The flavonoid compounds of citrus peels are expected to have anti-collagenase and anti-elastase activities.

The role of in silico studies in the discovery of new drugs is very important and interesting in the recent years, where the results can be used as confirmation of the results of in vitro tests carried out experimentally in the laboratory. One of the herbal ingredients is Ziziphus spina-christi leaves with effective antibacterial activity, such as for acne-causing bacteria, namely Propionibacterium acnes. This is because it contains main secondary metabolites with saponins as the major components which contain christinin as its active compound. There are four known types of christinin, namely christinin-A, christinin-B, christinin-C, and christinin-D. In this study, the molecular interaction of the christinin compound was tested to predict its affinity for Propionibacterium acnes compared to clindamycin, as well as to determine the level of safety on the skin so that it can be applied as a topical anti-acne dosage form. In silico studies, including molecular docking and toxicity prediction, were used to assess the activity of four molecules of the christinin compound on c-Jun N-terminal kinase (JNK) macromolecules. The christinin molecules form a strong and stable molecular interaction with the active site of the binding of c-Jun N-terminal kinase (JNK) macromolecules. Interestingly, the christinin compound molecules also has a fairly good level of safety based on the three identified parameters. Based on this results christinin compound molecules has potential to be developed as c-Jun N-terminal kinase (JNK) inhibitors candidate to control of skin infections caused by Propionibacterium acnes which has potential as a topical anti-acne.

The COVID-19 pandemic has become a serious problem today, with its prevalence increasing every day. The SARS-CoV-2 main protease (MPro) is a promising therapeutic target to inhibit replicating and spreading the virus that causes COVID-19. The compounds contained in the Etlingera elatior plant has the potential. This study aimed to examine the compounds' activity in E. elatior against SARS-CoV-2 MPro using in silico methods. A total of seven compounds contained in E. elatior were obtained from the Knapsack database. The compounds were then docked into the SARS-CoV-2 MPro receptor's active site with the PDB ID 6LU7. Afterward, the biological activities were predicted by the PASS prediction webserver. The molecular docking results showed that ergosterol peroxide and sitostenone had the best binding energy with -10.40 kcal/mol and -9.17 kcal/mol, respectively. The in silico PASS prediction showed it has potential as antiviral therapy. It concluded ergosterol peroxide and sitostenone has the potential as SARS-CoV-2 MPro inhibitor candidate.

Pendahuluan: Lendir kulit ikan lele kuning (Pelteobagrus fulvidraco), mengandung peptida bioaktif dan banyak dimanfaatkan dalam pengobatan berbagai penyakit karena memiliki aktivitas biologis, diantaranya sebagai antimikroba. Beberapa peptida bioaktif tersebut, antara lain pelteobagrin, myxinidin, pleurocidin, dan pardaxin-P1 dan telah terbukti mampu menghambat Penicillin-Binding Protein 3 (PBP3) dari Staphylococcus aureus. Tujuan: Penelitian ini bertujuan untuk mengidentifikasi aktivitas antimikroba molekul peptida bioaktif secara in silico terhadap makromolekul Penicillin-Binding Protein 3 (PBP3) dari Staphylococcus aureus dan interaksi peptida bioaktif tersebut yang terlibat dalam mekanisme aksi antimikroba. Metode: Sekuensing peptida bioaktif terlebih dahulu dilakukan pemodelan ke dalam bentuk konformasi 3D menggunakan software PEP-FOLD. Konformasi terbaik hasil pemodelan dipilih untuk kemudian dilakukan studi penambatan molekuler terhadap makromolekul dari Staphylococcus aureus menggunakan software PatchDock. Interaksi molekuler yang terbentuk selanjutnya diidentifikasi lebih lanjut menggunakan software BIOVIA Discovery Studio 2020. Hasil: Berdasarkan hasil penambatan molekuler menunjukkan bahwa peptida bioaktif myxinidin memiliki afinitas paling baik dengan ACE score −2497,26 kJ/mol. Kesimpulan: Peptida bioaktif lendir kulit ikan lele kuning (Pelteobagrus fulvidraco) dapat dipertimbangkan sebagai kandidat antimikroba alami.

Arabian bidara leaves (Ziziphus spina-christi, L.) are known to have strong antimicrobial activity against microorganisms that cause infection in the female genital area, namely Staphylococcus aureus bacteria and Candida albicans fungi. They contain main secondary metabolites such as flavonoids, alkaloids, and saponins. Christinin is a saponin glycoside derivative compound which consists of four types, namely christinin-A, B, C, and D. The role of computational studies in the discovery of new drugs is crucial and interesting nowadays because it is relatively cheap, effective, fast, and precise with a reliable level of accuracy. This computational study result will later be used to confirm in vitro test results which are carried out using experimental microbiological testing methods in the laboratory. This study identified, evaluated, and explored the interactions between christinin-A, B, C, and D compounds with Penicillin Binding Protein (PBP) from Staphylococcus aureus and Dihydrofolate Reductase from the fungus Candida albicans using computational study were carried out using the molecular docking. The christinin-A, B, C, and D compounds were modeled into 3D conformation using GaussView 5.0.8 and Gaussian09 software. The best conformation was selected for molecular interaction studies on Penicillin Binding Protein (PBP) from Staphylococcus aureus bacteria and Dihydrofolate Reductase from Candida albicans using MGLTools 1.5.6 software with AutoDock 4.2. The molecular interactions that occurred were further observed using the BIOVIA Discovery Studio 2020 software. Based on the molecular docking results, the christinin-B compound had the highest affinity for Penicillin Binding Protein (PBP) from Staphylococcus aureus bacteria, with a binding-free energy value of −7.67 kcal/mol. Meanwhile, the christinin-A compound has the highest affinity for Dihydrofolate Reductase from the fungus Candida albicans, with a binding-free energy value of −8.38 kcal/mol. Thus, it is predicted that christinin compounds can be chosen as the main component in feminine hygiene preparations to maintain the female genital area's health.

A pandemic coronavirus disease of 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now been declared a global pandemic by the World Health Organization. The search for new drugs, especially by utilizing antiviral peptides is a very potential area. Through this study, protein-peptide docking and protein-protein docking simulations were conducted using in silico methods to identify, evaluate, and explore the molecular affinity and interaction of dermaseptin peptide molecules produced by frogs of the genus Phyllomedusa against the SARS-CoV-2 spike protein macromolecule, and its effect on attachment to the surface of the ACE-2 (Angiotensin Converting Enzyme-2) receptor. Protein-peptide docking simulation results show that dermaseptin-S9 peptide molecule has the best affinity to the active site of SARS-CoV-2 spike protein macromolecule binding site, with a binding free energy value of −792.93 kJ/mol. Then the results of protein-protein docking simulations proved that dermaseptin-S9 peptide molecule was able to prevent the attachment of SARS-CoV-2 spike protein to the surface of the ACE-2 receptor, with a total energy value of 517.85 kJ/mol. Therefore, it is hoped that dermaseptin-S9 peptide molecule can be further studied in the development of novel antiviral peptide candidates for the control of COVID-19 infectious disease.

The recent public health crisis is threatening the world with the emergence of the spread of the new coronavirus 2019 (2019-nCoV) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This virus originates from bats and is transmitted to humans through unknown intermediate animals in Wuhan, China in December 2019. Advances in technology have opened opportunities to find candidates for natural compounds capable of preventing and controlling COVID-19 infection through inhibition of spike proteins of SARS-CoV-2. This research aims to identify, evaluate, and explore the structure of spike protein macromolecules from three coronaviruses (SARS-CoV, MERS-CoV, and SARS-CoV-2) and their effects on Angiotensin-Converting Enzyme 2 (ACE-2) using computational studies. Based on the identification of the three spike protein macromolecules, it was found that there was a similarity between the active binding sites of ACE-2. These observations were then confirmed using a protein-docking simulation to observe the interaction of the protein spike to the active site of ACE-2. SARS-COV-2 spike protein has the strongest bond to ACE-2, with an ACE score of ?1341.85 kJ/mol. Therefore, some of this information from the results of this research can be used as a reference in the development of competitive inhibitor candidates for SARS-CoV-2 spike proteins for the treatment of COVID-19 infectious diseases.

Glimepiride is often combined with metformin HCl as an oral antidiabetic in type II diabetes mellitus, which provides a complementary and synergistic effect with multiple targets for insulin secretion. Glimepiride includes class II of BCS, which solubility practically insoluble in water but high permeability, which will impact the drug's small bioavailability. In contrast, metformin HCl includes class III of BCS, which has a high solubility in water, but low permeability is absorbed approximately 50-60% in the digestive tract given orally. The co-crystallization method can be used to improve the glimepiride solubility properties and the permeability properties of metformin HCl by interrupting glimepiride with metformin HCl physically. This study aims to identify the physical interactions between glimepiride and metformin HCL using a thermal analysis of Differential Scanning Calorimetry (DSC) and then confirmed by a computational approach. Identifying the physical interactions between glimepiride and metformin HCL was carried out by plotting the melting points generated from the endothermic peaks of the DSC thermogram at various compositions versus the mole ratios of the two were further confirmed by the computational approach using PatchDock. The results of the phase diagram analysis of the binary system between glimepiride and metformin HCl show a congruent pattern, which indicates the formation of co-crystal or molecular compounds at a 1 : 1 mole ratio at 228°C. Computational approach results showed that the interaction between glimepiride and metformin HCl did not form new compounds but heterosinton formation that was stable in molecular dynamics simulations.

The emergence of multidrug-resistant Mycobacterium tuberculosis (MTB) has become a major problem in treating tuberculosis (TB) and shows the need to develop new and efficient drugs for better TB control. This study aimed to use in silico techniques to discover potential inhibitors to the Enoyl-[acyl-carrier-protein] reductase (InhA), which controls mycobacterial cell wall construction. Initially, 391 quercetin analogs present in the KNApSAck_3D database were selected, filters were sequentially applied by docking-based virtual screening. After recategorizing the variables (bond energy prediction and molecular interaction, including hydrogen bond and hydrophobic bond), compounds C00013874, C00006532, and C00013887 were selected as hit ligands. These compounds showed great hydrophobic contributions, and for each hit ligand, 100 ns of molecular dynamic simulations were performed, and the binding free energy was calculated. C00013874 demonstrated the greatest capacity for the InhA enzyme inhibition with ΔGbind = −148.651 kcal/mol compare to NAD (native ligand) presented a ΔGbind = −87.570 kcal/mol. These data are preliminary studies and might be a suitable candidate for further experimental analysis.