Arry Yanuar

Crystal structure of human Rad GTPase of the RGK-family.

Rad (Ras associated with diabetes) is an RGK‐family small GTPase that is over‐expressed in the skeletal muscle of humans with type II diabetes. Unlike other small GTPases, RGK family members including Rad lack several conserved residues in the GTPase domain. Here, we report the crystal structure of the GTPase domain of human Rad in the GDP‐bound form at 1.8 Å resolution. The structure revealed unexpected disordered structures of both switches I and II. We showed that the conformational flexibility of both switches is caused by non‐conservative substitutions in the G2 and G3 motifs forming the switch cores together with other substitutions in the structural elements interacting with the switches. Glycine‐rich sequences of the switches would also contribute to the flexibility. Switch I lacks the conserved phenylalanine that makes non‐polar interactions with the guanine base in H‐Ras. Instead, water‐mediated hydrogen bonding interactions were observed in Rad. The GDP molecule is located at the same position as in H‐Ras and adopts a similar conformation as that bound in H‐Ras. This similarity seems to be endowed by the conserved hydrogen bonding interactions with the guanine base‐recognition loops and the magnesium ion that has a typical octahedral coordination shell identical to that in H‐Ras.

Virtual screening of Indonesian herbal database as HIV-1 reverse transcriptase inhibitor

HIV-1 (Human immunodeficiency virus type 1) is a member of retrovirus family that could infect human and causing AIDS disease. AIDS epidemic is one of most destructive diseases in modern era. There were more than 33 million people infected by HIV until 2010. Various studies have been widely employed to design drugs that target the essential enzymes of HIV-1 that is, reverse transcriptase, protease and integrase. In this study, in silico virtual screening approach is used to find lead molecules from the library or database of natural compounds as HIV-1 reverse transcriptase inhibitor. Virtual screening against Indonesian Herbal Database using AutoDock4 performed on HIV-1 reverse transcriptase. From the virtual screening, top ten compounds were mulberrin, plucheoside A, vitexilactone, brucine N-oxide, cyanidin 3-arabinoside, alpha-mangostin, guaijaverin, erycristagallin, morusin and sanggenol N.

In Silico Approach to Finding New Active Compounds from Histone Deacetylase (HDAC) Family.

BACKGROUND Histone Deacetylase (HDAC) enzymes in the human body play an important role in the transcriptional regulation of gene expression. In the last decade, HDAC inhibitors and activators have been explored and have become known as therapeutic agents for many diseases such as osteodystrophy, neurogenerative disorders, cardiomyopathy, cancer, and diabetes. In recent years, the development of HDAC inhibitors or activators to obtain new potent lead compounds has been conducted using in vitro, in vivo, and in silico methods. Some HDAC family inhibitors and activators have been discovered. But some compounds have limitations such as not selectively binding to one of the HDAC variants. METHODS At present, through bioinformation, HDAC family sequences have been revealed, and some in silico methods such as molecular modelling (homology modelling and pharmacophore modelling), virtual screening, and molecular dynamics are widely used to find and develop new potent and selective compounds. RESULTS The main utilization of molecular modelling in this work is intended to complete the HDAC structure that partially lacks data regarding its amino acid monomer. Virtual screening methods are helpful in finding the best binding affinity of the test compounds. By molecular dynamic simulation, the temperature, time, and pressure can be adjusted to analyze the hydrogen bond. CONCLUSION Combining these in silico approaches will be a more effective and efficient solution in finding new lead compounds for HDAC drug discovery research in the future.

Virtual screening of 2,3-disubstituted-4(3H)-quinazolinones possessing benzenesulfonamide moiety for COX-2 inhibitor.

COX inhibitors which selectively inhibits the inducible COX-2 is an oenzyme that causes inflammation. They are clinically effective anti-inflammatory agents with less gastrointestinal and renal toxicity. However, they lack anti-thrombotic activity and hence lead to increased incidences of adverse cardiovascular trombotic events such as myocardial infarction. Therefore, there is still a need to develop better therapeutic effect and tolerability COX-2 inhibitor. The majority of COX-2 inhibitors are diaryl heterocycles. For optimum COX-2 selectivity and inhibitory potency a –SO3CH3 or a- SO2NH2 substituent at the para-position of phenyl ring was essential. A wide variety of heterocycles can serve as central ring system of the diaryl heterocycles structures. We report the screening of various 2,3-disubstituted-4(3H)-quinazolinones possessing benzenesulfonamide moiety, directly or indirectly bound to the ring system, using the Protein-Ligand ANT System (PLANTS) docking software against the COX-2 enzyme. Various molecular structures of ligands were docked and scored to identify structurally similar ligands to SC-558 (reference ligand) in binding interaction to COX-2 binding site. The results show that 2,3-disubstituted-4(3H)-quinazolinones possess pbenzenesulfonamide moiety at C-2, and phenyl moiety at N-3 binds directly or indirectly to the ring system with high binding affinity. The docked ligand has orientations similar to that observed with SC-558 satisfying Lipinskis rule of five.

Expression, purification, crystallization and preliminary crystallographic analysis of human Rad GTPase.

Human Rad is a new member of the Ras GTPase superfamily and is overexpressed in human skeletal muscle of individuals with type II diabetes. The GTPase core domain was overexpressed in Escherichia coli and purified for crystallization. Crystals were obtained at 293 K by vapour diffusion using a crystallization robot. The crystals were found to belong to space group P2(1), with unit-cell parameters a = 52.2, b = 58.6, c = 53.4 A, beta = 97.9 degrees , and contained two Rad molecules in the crystallographic asymmetric unit. A diffraction data set was collected to a resolution of 1.8 A using synchrotron radiation at SPring-8.

Synthesis and COX-2 Inhibitory Activity of 4-[(E)-2-(4-Oxo-3-phenyl-3,4-dihydroquinazolin-2-yl)ethenyl]benzene-1-sulfonamide and Its Analogs

Some novel 3-phenyl-2-[(E)-2-phenylethenyl]-3,4-dihydroquinazolin-4-one derivatives possessing para-sulfonamides groups on the phenyl ring of the 2-phenylethenyl moiety have been synthesized and their COX-2 inhibitory activity evaluated. The stuctures of the synthesized compounds were confirmed on the basis of FT-IR, 1H-NMR, 13C-NMR and mass spectral data. The COX-2 inhibition screening assay revealed that 4-[(E)-2-{3-(4-methoxyphenyl)-4-oxo-3,4-dihydroquinazolin-2-yl}ethenyl]benzene-1-sulfonamide had a maximum COX-2 inhibition (47.1%), at a concentration of 20 μM.

Pharmacophore-Based Virtual Screening from Indonesian Herbal Database to Finding New Inhibitor of HDAC4 and HDAC7

Objective: Nowadays, many researchers focused on finding and developing the new inhibitor of HDAC4 and HDAC7 using in silico tools such as docking, pharmacophore approaches, and molecular dynamics simulation. The aim of this research is to identify pharmacophore of HDAC4 and HDAC7. Method: In this research, pharmacophore-based virtual screening was used to find new HDAC4 and HDAC7 inhibitor from Indonesian herbal database. From MUBD-HDACs database, active compounds of HDAC4 and HDAC7 were divided into training and test set. Based on pharmacophore model generation for HDAC4 and HDAC7, 10 models were created. All the models were calculated and evaluated using some parameters of validation. Results: The best pharmacophore model for HDAC4 are model 6 and 10, and for HDAC7 is model 1. Pharmacophore model 6 and 10 (HDAC4) have seven pharmacophore features include three HBA, one HBD, one aromatic ring, one negatively ionizable area and 1 hydrophobic. Pharmacophore model 1 (HDAC7) have five pharmacophore features include two HBA, one HBD, one negatively ionizable area and one hydrophobic. These selected models for HDAC4 and HDAC7 were using for virtual screening against Indonesian herbal database. Conclusion: Based on the results of the virtual screening, six hit compounds were obtained such as artocarpesin, avicularin, dimboa glucoside, eriodictin, luteolin and mirabijalone c. Key words: Pharmacophore, Virtual Screening, HDAC4, HDAC7, Indonesian Herbal Database.

Review of angiotensin-converting enzyme inhibitory assay: Rapid method in drug discovery of herbal plants

The renin-angiotensin-aldosterone system is a signaling pathway which responsible in the blood pressure regulation. Angiotensin-converting enzyme (ACE) is one of the key elements responsible for the hypertensive mechanism. It converts angiotensin-I to angiotensin-II. The discovery history of the ACE inhibitory activity assay method has been through a long stage for decades and development continues until today. The ACE inhibitory activity has become an effective screening method in the search for new antihypertensive agents from herbal plants. Some of in vitro assay methods were used to examine the activity of ACE inhibitors based on the substrate usage, such as; Cushman and Cheung Method using a substrate hippuryl-histidyl-leucine (HHL), Holmquist method using a substrate furanacryloyl-tripeptide, Elbl and Wagner method using a substrate benzoil-[l-14C] glicyl-L-histidine-L-leucine, Carmel and Yaron method using a substrate o-aminobenzoylglycyl-p-nitrophenylalanilproline, and Lam method using 3-hydroxybutyrylglycyl-glycyl-glycine as substrate. Several different methods to measure the results of enzymatic reactions or separating substrate with products, including spectrophotometric, fluorometric, high-performance liquid chromatography, electrophoresis, and radiochemistry. Application of the test method for screening the ACE inhibitors activity and investigation of active compounds from natural products can be done easily with this method, it is very helpful in research because the results obtained are simple, accurate, and rapid.

Application of Ionic Liquid as a Green Solvent for Polyphenolics Content Extraction of Peperomia pellucida (L) Kunth Herb

Background: Inhibition of phosphodiesterase 4 (PDE4) is a promising therapeutic approach for the treatment of inflammatory pulmonary disorders i.e. asthma and chronic obstructive pulmonary disease. However, the treatment with PDE4 inhibitors is not definitive due to the side effects such as nausea and vomiting which are associated with the non-selective inhibitors. Objective: To identify selective PDE4B inhibitors that are expected to be potential drug candidates for the treatment of inflammatory pulmonary disorders. Methods: A shared feature pharmacophore model for both ligand and structure-based pharmacophore models for PDE4B inhibitors was developed and used as a query in the virtual screening of Maybridge and SPECS databases. The hits were filtered based on Lipinski’s rule of five and pharmacophore fit score. Finally, the hits were docked into the active site of PDE4B and PDE4D to test their affinity and selectivity. Results: Based on the virtual screening results, nine compounds were identified as final hits, where four compounds showed the highest affinity and selectivity for PDE4B over PDE4D according to the protein-ligand interactions analysis. Conclusion: Selective PDE4B inhibitors have been identified using a combination of pharmacophore-based virtual screening and molecular docking. Those inhibitors are promising candidates for pre-clinical evaluation to justify their affinity and selectivity for PDE4B and test their anti-inflammatory activity. Key words: Asthma, Chronic obstructive pulmonary disease, Molecular docking, Phosphodiesterase 4B, Virtual screening.Objectives: To find out the effect of mild heat shock on osteoblast proliferation and mineralisation following treatment with bisphosphonates. Materials and Methods: Cell culture of MC3T3 cells was performed in alpha minimum essential medium supplemented with 10% Foetal Calf Serum (FCS), 2 mmol L-glutamine and 100U/ml each of penicillin/streptomycin and were incubated at 37°C in humidified 5% CO2. The selected bisphosphonate drugs were administered, following which heat therapy was given by placing the flasks in a temperature-regulated water bath. The proliferation of osteoblast progenitors was measured using the methylene blue staining technique. Results: The results showed that mild heat-shock for 2 min at 42°C can stimulate proliferation of osteoblast progenitors, as well as bone nodule formation. In addition, mild heat-shock can reverse the action of bisphosphonate by stimulation of osteoblast proliferation and mineralisation. Conclusion: Mild heat-shock enhances cell differentiation and osteoblasts mineralisation following bisphosphonate treatment. Key words: Bisphosphonates, Heat-shock, Osteoblast, Osteoclast.

A Preliminary Study on Shifting from Virtual Machine to Docker Container for Insilico Drug Discovery in the Cloud

The rapid growth of information technology and internet access has moved many offline activities online. Cloud computing is an easy and inexpensive solution, as supported by virtualization servers that allow easier access to personal computing resources. Unfortunately, current virtualization technology has some major disadvantages that can lead to suboptimal server performance. As a result, some companies have begun to move from virtual machines to containers. While containers are not new technology, their use has increased recently due to the Docker container platform product. Docker’s features can provide easier solutions. In this work, insilico drug discovery applications from molecular modelling to virtual screening were tested to run in Docker. The results are very promising, as Docker beat the virtual machine in most tests and reduced the performance gap that exists when using a virtual machine (VirtualBox). The virtual machine placed third in test performance, after the host itself and Docker.