HIV molecule we have carried out mo

HIV molecule we have carried out molecular docking studies on some succinic acid
derivatives. The ligand interaction diagram and binding energies of these molecules have
been drawn and compared with efavirenz. The docking studies have been done on the protein
having PDB ID 1FK9. The druggability of succinic acid derivative which has highest binding
energy with the HIV reverse transriptase was determined. The drug similar to the succinic
acid derivative were also identified using quick prop program. The drugs presently used in
the treatment of other diseases which were found similar to the best succinic acid derivatives
were also subjected to molecular docking studies with the same reverse transcriptase. In this
paper we report the results of these molecular dockings and the drug properties of these
molecules
2. MATERIAL AND METHODS
The molecular docking studies were carried out on glide 5.0 of Schrodinger 2012 software.
The druggability was also studied with the help of quick prop program of the same software.
The protein PDB ID 1FK9 was downloaded from site RCSB.org. The structures of succinic
acid derivatives synthesized by Tayde[24] were drawn on Chem Draw .
The HIV protein IFK9 is a crystal of reverse transcriptase complexed with efavirenz. The
crystal of this protein has been determined by X-Ray diffraction studies. The resolution is
2.50 Ao . The formula weight of the polymeric material is 57399.6. It has two chains . A chain
has formula weight 62789.6. It is a polypeptide and has p66 fragment. The B chain is also a
polypeptide . The formula weight is 51399.6. The fragment is p51. The definite sequence of
amino acids in each chain can be found at RSCB.org.
3. Computational studies
The molecular docking studies were done on the HIV-1RT PDB ID-IFK9 by downloading it
on the glide software of Schrodinger 2012. The validation of the docking protocol was
carried out by removing the co-crystallized efavirenz from the binding site and re-docking it
to the IFK9. We found very good agreement between the localization of the inhibitor
efavirenz upon docking and from crystal structure. The relative mean square deviation
(RMSD) between the predicted conformation and the observed X-Ray crystallography of
efavirenz equaled 1.02 A0. This indicated the reliability of the docking method in reproducing
the experimentally observed binding mode for HIV-1RT.

Results (Indonesian) 2:

Molekul HIV kami telah melakukan penelitian molecular docking pada beberapa asam suksinat
derivatif. Diagram interaksi ligan dan energi mengikat molekul-molekul ini telah
digambarkan dan dibandingkan dengan efavirenz. Studi docking telah dilakukan pada protein
memiliki PDB ID 1FK9. The druggability dari turunan asam suksinat yang tertinggi mengikat
energi dengan transriptase terbalik HIV ditentukan. Obat mirip dengan suksinat
turunan asam juga diidentifikasi menggunakan program prop cepat. Obat saat ini digunakan di
pengobatan penyakit lain yang ditemukan mirip dengan turunan asam suksinat terbaik
juga menjadi sasaran studi docking molekular dengan reverse transcriptase yang sama. Dalam hal ini
kertas kami melaporkan hasil ini dockings molekul dan sifat obat ini
molekul
2. BAHAN DAN METODE
Penelitian docking molekuler dilakukan pada glide 5.0 dari 2.012 software Schrodinger.
Druggability itu juga belajar dengan bantuan program prop cepat dari perangkat lunak yang sama.
Protein PDB ID 1FK9 diunduh dari situs RCSB.org. Struktur suksinat
turunan asam disintesis oleh Tayde [24] digambar di Chem Draw.
The IFK9 protein HIV adalah kristal reverse transcriptase kompleks dengan efavirenz. The
kristal protein ini telah ditentukan oleh studi difraksi X-Ray. Resolusi
2,50 Ao. Berat rumus dari bahan polimer adalah 57.399,6. Ini memiliki dua rantai. Sebuah rantai
memiliki rumus berat 62.789,6. Ini adalah polipeptida dan memiliki P66 fragmen. Rantai B juga
polipeptida. Rumus berat 51.399,6. Fragmen adalah P51. Urutan pasti
asam amino di masing-masing rantai dapat ditemukan di RSCB.org.
3. Studi komputasi
Studi docking molekuler dilakukan pada HIV-1RT PDB ID-IFK9 dengan mengunduhnya
dari software luncur Schrodinger 2012. Validasi protokol docking itu
dilakukan dengan menghapus co-kristalisasi efavirenz dari situs mengikat dan re -docking itu
untuk IFK9 tersebut. Kami menemukan kesepakatan yang sangat baik antara lokalisasi inhibitor
efavirenz pada docking dan dari struktur kristal. Relatif rata penyimpangan persegi
(rmsd) antara konformasi diprediksi dan diamati X-Ray kristalografi dari
efavirenz menyamai 1.02 A0. Hal ini menunjukkan keandalan metode docking dalam mereproduksi
modus mengikat eksperimen diamati untuk HIV-1RT.