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CRS-ForMIND International Conference 2017 - Call for Papers

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Page 1, data 1 to 10 of 43, displayed in 10 data per page
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1.

In silico study of porphyrin-anthraquinone hybrids as CDK2 inhibitor

Muhammad Arba, Sunandar Ihsan, La Ode Ahmad Nur Ramadhan, Daryono Hadi Tjahjono
Elsevier (2017)

Muhammad Arba (3 records)

Abstract
Cyclin-Dependent Kinases (CDKs) are known to play crucial roles in controlling cell cycle progression of eukaryotic cell and inhibition of their activity has long been considered as potential strategy in anticancer drug research. In the present work, a series of porphyrin-anthraquinone hybrids bearing mesosubstituents, i.e. either pyridine or pyrazole rings were designed and computationally evaluated for their Cyclin Dependent Kinase-2 (CDK2) inhibitory activity using molecular docking, molecular dynamics simulation, and binding free energy calculation. The molecular docking simulation revealed that all six porphyrin hybrids were able to bind to ATP-binding site of CDK2 and interacted with key residues constituted the active cavity of CDK2, while molecular dynamics simulation indicated that all porphyrins bound to CDK2 were stable for 6 ns. The binding free energies predicted by MM-PBSA method showed that most compounds exhibited higher affinity than that of native ligand (4-anilinoquinazoline, DTQ) and the affinity of mono-H2PyP-AQ was about three times better than that of DTQ, indicating its potential to be advanced as a new CDK2 inhibitor.

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2.

Molecular modeling of cationic porphyrin-anthraquinone hybrids as DNA topoisomerase IIβ inhibitors

Muhammad Arba, Ruslin, Sunandar Ihsan, Setyanto Tri Wahyudi, Daryono H.Tjahjono
Elsevier (2017)

Muhammad Arba (3 records)

Abstract
Human DNA Topoisomerase II has been regarded as a promising target in anticancer drug discovery. In the present study, we designed six porphyrin-anthraquinone hybrids bearing pyrazole or pyridine group as meso substituents and evaluated their potentials as DNA Topoisomerase IIb inhibitor. First, we investigated the binding orientation of porphyrin hybrids into DNA topoisomerase IIb employing AutoDock 4.2 and then performed 20-ns molecular dynamics simulations to see the dynamic stability of each porphyrin-Topo IIb complex using Amber 14. We found that the binding of porphyrin hybrids occured through intercalation and groove binding mode in addition interaction with the amino acid residues constituting the active cavity of Topo IIb. Each porphyrin-Topo IIb complex was stabilized during 20-ns dynamics simulations. The MM-PBSA free energy calculation shows that the binding affinities of porphyrin hybrids were modified with the number of meso substituent. Interestingly, the affinity of all porphyrin hybrids to Topo IIb was stronger than that of native ligand (EVP), indicating the potential of the designed porphyrin to be considered in experimental research

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3.

Molecular modeling on porphyrin derivatives as b5 subunit inhibitor of 20S proteasome

Muhammad Arbaa, Andry Nur-Hidayat, Ruslin, Muhammad Yusuf, Sumarlin, Rukman Hertadi, Setyanto Tri Wahyudi, Slamet Ibrahim Surantaadmaja, Daryono H. Tjahjono
Elsevier (2018)

Muhammad Arba (3 records)

Abstract
The ubiquitin-proteasome system plays an important role in protein quality control. Currently, inhibition of the proteasome has been validated as a promising approach in anticancer therapy. The 20S core particle of the proteasome harbors b5 subunit which is a crucial active site in proteolysis. Targeting proteasome b5 subunit which is responsible for the chymotrypsin-like activity of small molecules has been regarded as an important way for achieving therapeutics target. In the present study, a series of porphyrin derivatives bearing either pyridine or pyrazole rings as meso-substituents were designed and evaluated as an inhibitor for the b5 subunit of the proteasome by employing molecular docking and dynamics simulations. The molecular docking was performed with the help of AutoDock 4.2, while molecular dynamics simulation was done using AMBER 14. All compounds bound to the proteasome with similar binding modes, and each porphyrin-proteasome complex was stable during 30 ns MD simulation as indicated by root-mean-square-deviation (RMSD) value. An analysis on protein residue fluctuation of porphyrin binding demonstrates that in all complexes, porphyrin binding produces minor fluctuation on amino acid residues. The molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation shows that the binding affinities of mono-H2PyP, bis-H2PzP, and tetra-H2PyP were comparable with that of the potential inhibitor, HU10. It is noted that the electrostatic interaction increases with the number of meso-substituents, which was favourable for porphyrin binding. The present study shows that both electrostatic and van der Waals interaction are the main force which controls the interaction of porphyrin compounds with the proteasome.

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4.

Identification of UDP-glucose binding site in glycosyltransferase domain of sucrose phosphate synthase from sugarcane (Saccharum officinarum) by structure-based site-directed mutagenesis

Widhi Dyah Sawitri, Siti Nurul Afidah, Atsushi Nakagawa, Toshiharu Hase, Bambang Sugiharto
Biophysical Reviews (2018)

Widhi Dyah Sawitri (2 records)

Abstract
Sucrose phosphate synthase (SPS) is believed to be the key enzyme for controlling the biosynthesis of sucrose. SPSs consist of a functional glycosyltransferase domain that shares conserved residues with the glycosyltransferase domain of sucrose biosynthesis- related protein. The formation of sucrose-6-phosphate is catalyzed by SPS with the transfer of a glycosyl group of uridine diphosphate glucose (UDP-G) as an activated donor sugar to a fructose-6-phosphate as a sugar acceptor. However, understanding of the mechanism of catalytic and substrate binding in SPS is very limited. Based on amino acid sequence alignments with several enzymes that belong to the glycosyltransferase family, the UDP-G binding sites that might be critical for catalytic mechanism were identified. Here, we report that single point mutation of R496, D498, and V570 located in the proposed UDP-G binding site led to less active or complete loss of enzyme activity. Through structure-based site-directed mutagenesis and biochemical studies, the results indicated that these residues contribute to the catalytic activity of plant SPS. Moreover, understanding of the UDP-G binding site provides an insight into new strategies for enzyme engineering and redesigning a catalytic mechanism for UDP.

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5.

Desain Pengembangan Modul Kebakaran Hutan Dan Lahan Pada Tingkat Pendidikan Menengah Di Provinsi Riau

Rudy Haryanto, Suwondo, Siti Sacharisa
SEMIRATA 2017 BIDANG MIPA BKS-PTN WILAYAH BARAT (2017)

Rudy Haryanto (3 records)

Abstract
Land and forest fires is an environmental problem that occurred in Riau Province. Lack of knowledge and understanding the danger of land and forest fires and the importance of land and forest management became one of the causes of forest fire control measures are not optimal. Education is expected to generate alternative prevention through integration of learning in high school. The study consists of several stages: Analysis, Design and Development. The data collection was performed using literature study, observation and interviews, data analysis conducted by qualitative descriptive. The results of data analysis showed that there are Core Competencies and the Basic Competencies in X grade biology lesson that can be integrated with land and forest fires material. Design module is based on the Basic Competence to analyze the data of environmental changes, causes and the impact on lives. The development phase conducted with validation and limited testing of the modules. The results obtained showed that the developed module design of land and forest fires can be used as the enrichment material for learning in high school. Keywords: Design Module Development, Land and Forest Fires, Secondary Education, Riau Province.

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6.

Implementation of Environmental Education to Support Sustainability of Green Campus Program in Universitas Riau

Suwondo, Darmadi, Rudy Haryanto
Proceeding: The 1st - UR International Conference on Educational Science s (2017)

Rudy Haryanto (3 records)

Abstract
Education strategy through implementation of Environmental Education (EE) was implemented to achieve sustainability of green campus program in Universitas Riau. The learning process is done so that students have knowledge and attitude to applied in life. The research was conducted by survey method with measured parameters is the success rate of the learning process (planning, implementation and learning outcomes) and student attitudes toward the campus environment. Respondents are lecturers and students who have attended EE. Data were collected by observation, questionnaires, and documentation, which were analyzed descriptively. The results showed that the learning process of EE has a good with the students knowledge is good. The attitude of the students after attending the lecture also shows a good response to environmental management.

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7.

Profil Kualitas Perairan Sungai Siak Berdasarkan Bioindikator Plankton dan Bentos

Rudy Haryanto, Syaris Kamaludin, Suwondo, Yuslim Fauziah
Prosiding: Seminar Nasional Pengelolaan Daerah Aliran Sungai Secara Terpadu 2017 (2017)

Rudy Haryanto (3 records)

Abstract
The decrease in river quality has occurred a lot. Siak River is a large river where its entire tream (upstream to downstream) is in Riau Province. This research was to know the uality of Siak River based on plankton and benthos bioindicator. Determination of research station was by purposive random sampling with 6 research station which as upstream, middle, downstream, and estuary. Each station consisted 3 sampling point sampled. Biology parameters were composition types, diversity index, and saprobic index. Physical and chemical parameters including temperature, brightness, current velocity, Dissolved Oxygen (DO), Biological oxygen demand (BOD), Chamical Oxygen Demand (COD), pH, salinity, substrate texture, and substrate organic content. The result of research showed that the quality of Siak River based on plankton and benthos bioindicator was good and bad to worse with low and high to severe levels polluted. The river was good quality on upstream, to the downstream worse.

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8.

Ladang berpindah dan model pengembangan pangan Indonesia: studi kasus daerah dengan teknik ladang berpindah dan pertanian modern

Muhammad Rifqi
National Conference Innovation and Application of Technology in Industry (2017)

Muhammad Rifqi (1 records)

Abstract
Ladang berpindah telah dilakukan sejak 10.000 tahun sebelum masehi oleh masyarakat adat. Banyak anggapan bahwa ladang berpindah adalah kegiatan primitif yang merusak hutan. Akan tetapi, pada beberapa kasus, perladangan berpindah justru mampu mempertahankan keanekaragaman hayati ekosistem di sekitarnya. Review paper ini bertujuan untuk mempelajari konsep dasar teknik perladangan berpindah yang dilakukan oleh masyarakat adat di Dusun Sungai Utik, Kalimantan Barat, serta perbedaannya dengan sistem pertanian modern di Kecamatan Bawen, Semarang. Hasil review menunjukkan bahwa sebagian besar teknik pertanian modern berpotensi merusak ekosistem. Sebanyak 75% danau Rawa Pening telah rusak akibat invasi enceng gondok (Eichornia crassipes) akibat suplai nutrien berlebih yang masuk ke dalam danau oleh kegiatan pertanian modern berskala besar. Sistem monokultur pada pertanian modern juga berdampak pada meningkatnya populasi hama. Model pengembangan pertanian modern berkelanjutan menekankan pada sistem pertanian polikultur. Keanekaragaman predator yang lebih tinggi pada pertanian polikultur mampu mengendalikan populasi hama. Pengendalian biologis terhadap hama dapat menurunkan tingkat penggunaan pestisida yang tidak ramah lingkungan. Penggunaan konsep ladang berpindah dalam sistem pertanian modern dapat menjadi solusi atas permasalahan pangan di Indonesia.

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9.

THE INFLUENCE OF COOPERATIVE INTEGRATED RAEDING AND COMPOSITION (CIRC) MODEL TROUGH THE RESULT IN READING AND WRITING SKILL IN THE DEAF CHILDREN

Muhammad Nurrohman Jauhari (2 records)

Abstract
Reading and writing is a kind of skull in written language. Trough the written language someone got information, got science and also got knowledge. The deaf children has a lack in reading and writing. From observation in five grade SDLB – B KaryaMulia I Surabaya, skill a reading and writing deaf children is still lower. The researcher has big hope toslove this problem by using Cooperative Integrated Raeding And Composition (CIRC) model. This research in reading and writing skill. The research supposed to analyze the influence of using Cooperative Integrated RaedingAnd Composition (CIRC) model trough the result in reading and writing skill the student of five grade in SDLB – B KaryaMulia I Surabaya The study in quantitative research which used pre experiment. Research used one group pre – test and post – test. Method the data was obtained and test. The data analyzed use non parametric statistic. The result from pre – test is 33,3 after giving intervension for 8 time in 75 minutes every time. The result post – test is 73,9. Analyze in sign test (Zh) while the table 5% two side 1,96 the result is 2,47. It means there is influence in using Cooperative Integrated RaedingAnd Composition (CIRC) model trough the reading and writing skill in five grade of SDLB – B KaryaMulia I Surabaya

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10.

Development Of Symbols Signalong Indonesia As A Media Communication Children With Special Needs

Muhammad Nurrohman Jauhari (2 records)

Abstract
The use of symbols as a medium of communication for children with special needs still exist in Indonesia. At this time Indonesia uses the existing symbols are acceptable under international conventions, such as the symbols of the traffic in the form of symbols, letters, numbers, words, or a combination of them that serves as a warning, prohibition, orders or instructions. The problems that arise at this point is the absence of a symbol signalong Indonesia as visual support in understanding words on cue signalong Indonesia. This study aims to produce prototype Symbol Signalong Indonesia For Media Communication Children with Special Needs as visual cues support signalong Indonesia. Goals from Indonesia signalong symbols are special needs children who have communication barriers, obstacles and barriers motoric intelligence. Methods of data collection in this research is using Likert scale and questionnaire. Research development development model Borg and Gall (2007) on the adaptation of the development model of Dick and Carey. The quantitative data obtained from the scores given by the validator. The qualitative data obtained from the comments and suggestions validator is used to repair symbol Signalong Indonesia. Prototype symbol signalong Indonesia produces 159 symbols in accordance with Indonesian culture in the pack in the form of a book. Expert validation symbol indicates that the symbol Signalong Indonesia otherwise very decent. The results of analysis of the feasibility of signalong Indonesia given a score of 5 and Validation practitioners signalong Indonesia gesture shows that the symbol Signalong Indonesia otherwise very decent. The results of analysis of the feasibility of signalong Indonesia given a score of 4.75

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