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The target for COVID-19 has been successfully crystallized along with its inhibitor, named SARS-CoV-2 main protease, making it easier for drug discovery and development. Sponge (Clathria Sp.) is a marine species that can be found in Indonesia and has a unique chemical structure that is still rarely explored in its properties. Therefore, this study aims to examined the potential of marine natural products from sponge (Clathria Sp.) as SARS-CoV-2 main protease inhibitor using in silico method. The ligand structures were obtained from the Knapsack database and the protein structure obtained from the RCSB site with the PDB code: 6LU7. The molecular docking method was validated by re-docked the native ligand and calculated the RMSD value. The compounds contained in Sponge were docked into the active site of the protein based on the validated methods. Afterward, the molecular dynamics were performed for 100 ns simulation, then analyzed its system complex stability. The RMSD 1.329 A was obtained by re-docked of native ligand which indicates that the docking method was valid. Molecular docking of the ligands showed mirabilin_G has binding energy -7.38 kcal/mol, compared to the native ligand N3 inhibitor that is -7.30 kcal/mol, and the ligand showed good stability from molecular dynamics simulation indicated by RMSD, RMSF and MM-PBSA binding free energy similar to the inhibitor during 100 ns simulation. Its indicated the potential of the compounds contained in the sponge as inhibitor of SARS-CoV-2 main protease.Communicated by Ramaswamy H. Sarma.

Tyrosinases are essential metal-containing enzymes in the biosynthesis of melanin, therefore responsible for pigmentation of the skin. The upregulation of tyrosinase enzyme activities leads to hyperpigmentation that will become a health problems and interfere psychosocially. Inhibition of tyrosinase enzyme activity, both competitive and non-competitive become widely developed for most anti hyperpigmentation agent. Natural antioxidants are one of the potential compounds for this purpose. Red grape seeds contain high levels of antioxidant compounds, such as procyanidin, prodelphinidin, and propelargonidin. In this research in silico studies, including molecular docking, molecular dynamics simulations, and toxicity predictions, were used to assess the activity of the three molecules of polyphenolic compounds on macromolecules of the tyrosinase enzyme. Molecular docking studies show that the compound propelargonidin has the highest affinity against the macromolecule of the tyrosinase enzyme, with a binding free energy value of −32.87 kJ/mol. These results were confirmed in molecular dynamics simulations that show strong interactions at the macromolecular active site of the tyrosinase enzyme. Toxicity prediction results show that the three polyphenolic compound molecules were classified in the High-Class Category, which shows that safety is not guaranteed, but is likely, not carcinogenic and nongenotoxic. Therefore, the compound propelargonidin is predicted to be able to interact strongly with the tyrosinase enzyme. The results in this research are useful for further study in the development of tyrosinase enzyme inhibitors.

The 2019 coronavirus pandemic disease (COVID-19) is still declared a global pandemic by the World Health Organization (WHO). Therefore, an effort that is considered effective in finding therapeutic agents is needed to prevent the spread of COVID-19 infection. One of the steps that can be chosen is by utilizing antimicrobial peptides (AMPs) from animal venom by targeting the specific receptor of SARS-CoV-2, namely the main protease (Mpro). Through this research, a computational approach will be conducted to predict antiviral activity, including protein-peptide docking using PatchDock algorithm, to identify, evaluate, and explore the affinity and molecular interactions of four types of antimicrobial peptides (AMPs), such as Mucroporin, Mucroporin-M1, Mucroporin-S1, and Mucroporin-S2 derived from scorpion venom (Lychas mucronatus) against main protease (Mpro) SARS-CoV-2. These results were then confirmed using protein-peptide interaction dynamics simulations for 50 ns using Gromacs 2016 to observe the molecular stability to the binding site of SARS-CoV-2 Mpro. Based on protein-peptide docking simulations, it was proven that the Mucroporin S-1 peptides have a good affinity against the active site area of SARS-CoV-2 Mpro, with an ACE score of −779.56 kJ/mol. Interestingly, Mucroporin-S1 was able to maintain the stability of its interactions based on the results of RMSD, RMSF, and MM/PBSA binding free energy calculations. The results of the computational approach predict that the Mucroporin-S1 peptide is expected to be useful for further research in the development of new antiviral-based AMPs for the COVID-19 infectious disease.

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.

Background: The emergence of infectious diseases caused by SARS-CoV-2 has resulted in more than 90,000 infections and 3,000 deaths. The coronavirus spike glycoprotein encourages the entry of SARS-CoV-2 into cells and is the main target of antivirals. SARS-CoV-2 uses ACE2 to enter cells with an affinity similar to SARS-CoV, correlated with the efficient spread of SARS-CoV-2 among humans.Objective: In the research, identification, evaluation, and exploration of the structure of SARS-CoV and SARS-CoV-2 spike glycoprotein macromolecules and their effects on Angiotensin-Converting Enzyme 2 (ACE-2) using in silico studies.Methods: The spike glycoproteins of the two coronaviruses were prepared using the BIOVIA Discovery Studio 2020. Further identification of the three-dimensional structure and sequencing of the macromolecular spike glycoprotein structure using Chimera 1.14 and Notepad++. To ensure the affinity and molecular interactions between the SARS-CoV and SARS-CoV-2 spike glycoproteins against ACE-2 protein-protein docking simulations using PatchDock was accomplished. The results of the simulations were verified using the BIOVIA Discovery Studio 2020.Results: Based on the results of the identification of the macromolecular structure of the spike glycoprotein, it was found that there are some similarities in characteristics between SARS-CoV and SARS-CoV-2. Protein-protein docking simulations resulted that SARS-COV-2 spike glycoprotein has the strongest bond with ACE-2, with an ACE score of −1509.13 kJ/mol.Conclusion: Therefore, some information obtained from the results of this research can be used as a reference in the development of SARS-CoV-2 spike glycoprotein inhibitor candidates for the treatment of infectious diseases of COVID-19.

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.

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.

Anticoagulants are very important for the treatment and prevention of thrombotic disorders. The use of conventional anticoagulants like heparin and warfarin can cause bleeding complications. To find safer anticoagulant therapy agents, the development of isolation of new anticoagulant compounds has shifted towards natural sources. Bioactive peptides can be considered a better alternative because of their therapeutic potential in the treatment of various diseases. Several peptide molecules have been shown to inhibit the cytochrome P450 (CYP) 2C9 enzyme as a natural anticoagulant, such as bioactive peptides produced by yellowfin sole (Limanda aspera) and bioactive peptides in blue mussel (Mytilus edulis). This study aims to identify and evaluate the interactions that occur between peptide molecules with the cytochrome P450 (CYP) 2C9 enzyme using protein-peptide docking methods. Bioactive peptide sequencing was modeled using the PEP-FOLD software. The best conformation was chosen for an interaction study against the macromolecule of cytochrome P450 (CYP) 2C9 enzyme using PatchDock software. Further observations were made of interactions formed using BIOVIA Discovery Studio 2020 software. Based on the results of protein-peptide docking, the yellowfin sole peptide molecule has a good affinity against the macromolecule of cytochrome P450 (CYP) 2C9 enzyme, with an ACE score of −2527.01 kJ / mol. Therefore, the bioactive peptide is predicted to be used as a candidate for the cytochrome P450 (CYP) 2C9 enzyme inhibitor.

The new coronavirus (SARS-CoV-2), which caused the global pandemic Coronavirus Disease-2019 (COVID-2019), has infected nearly 206 countries. There is still little information about molecular compounds that can inhibit the development of infections caused by this disease. It is crucial to achieving the discovery of competent natural inhibitor candidates, such as antiviral peptides, because they have a variety of biological activities and have evolved to target biochemical machinery from different pathogens or host cell structures. In silico studies will be carried out, including protein-peptide docking and protein-protein docking, to identify, evaluate, and explore the affinity and molecular interactions of the Magainin-1 and Magainin-2 peptide molecules derived from frog skin (Xenopus laevis) to the main protease macromolecule (Mpro) SARS-CoV-2, and its effect on the ACE-2 receptor (Angiotensin Converting Enzyme-2 Receptor). Protein-peptide docking simulations show that both peptide molecules have a good affinity for the active site area of the SARS-CoV-2 Mpro macromolecule. These results were then confirmed using protein-protein docking simulations to observe the ability of the peptide molecule in preventing attachment to the ACE-2 receptor surface area. In silico studies show that Magainin-2 has the best affinity, with a bond free energy value of −3054.53 kJ/mol. Then the protein-protein docking simulation provided Magainin-2 was able to prevent the attachment of ACE-2 receptors, with an ACE score of 1697.99 kJ/mol. Thus, through in silico research, it is hoped that the Magainin peptide molecule can be further investigated in the development of new antiviral peptides for the treatment of infectious diseases of COVID-19.

The data collected in the present work correspond to the behavioral, Hepatosomatic Index (HSI), Gonadosomatic Index (GSI) and total lipid analysis between male and female mud crabs, Scylla olivacea at different water velocities. A total of 56 immature male and female crabs were used in this data article. The important criteria for estimating the selective habitat facing by S. olivacea is a considerate of (1) the behavioral range in response to abiotic factors (and how it adapt ontogenetically) and (2) the movement of the crab under wild velocities situations. This work purposes to recognize the performance, locomotion rate and escaping capability of S. olivacea under stagnant and flowing water situations and to discuss the significance of horizontal walking to habitat choice. The collective outcomes clearly show that the locomotor activities and escaping capabilities of S. olivacea were influenced by water flow in the mangrove habitats. For the HSI data, velocities of 20 cm/s were the highest increased mean HSI percentage and highest mean HSI percentage in males and females was recorded on the end of the experiment. For GSI percentage of male and female crabs, 20 cm/s dominates the highest increases mean GSI, followed by 60, 40 and 0 cm/s. For total lipid percentage, the results showed that, the mean total lipid of hepatopancrease, muscle and gonad were increased at the beginning and decreased at the final in each water velocities except for 20 cm/s over a culture period of 60 days. Velocities of 20 cm/s were the highest increased mean total lipid percentage followed by 40, 60, and lastly 0 cm/s. The high flow velocities inhibit the production of hepatopancrease and gonad, in terms of nutrients from food used to endeavor the stress condition faced. Keywords: Aquaculture, Biochemical changes, Comparison between sexes, Hydrodynamic, Portunid crab

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.

Population density, growth, survival, water quality and larval stage index of purple mud crab, Scylla tranquebarica at different feeding regimes and the data on ingestion rate of chosen microalgae, survival and larval development of blue swimming crab, Portunus pelagicus are presented. A twenty days of S. tranquebarica larval culture from zoeal 1 until megalopa stage under two different feeding regimes of A) Rotifer, Artemia nauplii and shrimp meat and B) Rotifer, Artemia nauplii and artificial feed is shared. A method on investigation of individual larvae of P. pelagicus capability to catch four different types of microalgae within 24 h is also shared. Direct eye observation, data collected through the larval rearing culture of S. tranquebarica and further statistical analysis were done daily until the crabs reached the megalopa stage. The result obtained from the optimum density of selected microalgae fed by individual larvae of P. pelagicus will be combined with the highest survival rate and larval stage index to develop feeding schedule for crab larvae P. pelagicus. This dataset has not previously been published and is of great potential for further comparison with other – and future investigation of various feeding regimes affected the crab culture. The collected information could be used as a standard feeding regime for nursery and hatchery seed production of others portunids crabs. The data described in this article are available as a supplementary file to this article. Keywords: Aquaculture, Crablet, Development, Growth, Larval rearing, Scylla tranquebarica, Portunus pelagicus, Microalgae selection

Objective: Prostate cancer is the second most common cancer in men. One of the efforts in the treatment of prostate cancer is by inhibiting histone lysine demethylase. Derivative compounds of coumarine, N-oxalylglycine, organoselenium, organosulfur, and pyridine have been reported to be active against two types of histone lysine demethylase (KDM) enzymes, KDM4E and KDM5B. This study aims to study the interactions of these derivatives with KDM.Methods: In this study, we performed computational studies, including molecular docking and molecular dynamics (MDs) simulations, and toxicity prediction, to assess the compounds’ activities toward three other KDM enzymes, KDM1A, KDM4A, and KDM4C.Results: Molecular docking simulations showed that a derivative compound of N-oxalylglycine, (R)-3-(4-[benzyloxy]phenyl)-2-(carboxyformamido) propanoic acid, and a derivative compound of pyridine, 3-(4-methoxybenzylamino)pyridine-2,4-dicarboxylic acid, has the highest affinity toward KDM. These results were confirmed in MDs studies which showed strong interactions at the active site of the five receptors. Toxicity prediction results show that the derivative compounds of coumarine, N-oxalylglycine, organoselenium, organosulfur, and pyridine are classified in category (high class), which suggests that the safety is not guaranteed, but is likely, not carcinogenic and nongenotoxic.Conclusion: Several coumarin, N-oxalylglycine, organoselenium, organosulfur, and pyridine derivative compounds are predicted to be able to interact strongly with KDM. The results in this study are useful for further studies in the development of novel anticancer drugs that target KDM.