Pemodelan interaksi antibiotik baru turunan eritromisin (Anhidroeritromisin-A, MFE dan MMFE) terhadap rRNA 23S Deinoccus radiodurans serta prediksi potensi antibiotiknya

HARYADI, Winarto, Promotor Prof. Dr. Umar Anggara Jenie, M.Sc., Apt

2010 | Disertasi | S3 Bioteknologi

Pemodelan interaksi molekul antibiotik terhadap rRNA 23S Deinococcus radiodurans dilakukan pada tiga turunan baru eritromisin (Δ6-Anhidroeritromisin-A, 3- O-mikarosil-5-O-forosominil eritronolid-B (MFE) and 3-O-mikarosilmikaminosil-5-Oforosominil eritronolid-B (MMFE)) untuk memprediksi potensi antibiotiknya. Δ6-Anhidroeritromycin-A dibuat melalui rekayasa biosintesis sedangkan MFE dan MMFE dibuat dengan cara biosintesis hibrid. Pemodelan interaksi juga dilakukan terhadap eritromisin-A, klaritromisin, roksitromisin, spiramisin and kloramfenikol serta eritronolid-A and 6-deoksieritromisin-A sebagai pembanding. Struktur eritromisin-A, klaritromisin, roksitromisin dan kloramfenikol diperoleh melalui penelusuran situs Protein Data Bank dengan kode PDB 1JZX. Struktur molekul tersebut merupakan kompleks interaksi molekul-molekul antibiotik dengan rRNA 23S Deinococcus radiodurans berdasarkan hasil kristalografi sinar-X. Struktur spiramisin diperoleh dari hasil penelusuran dengan kode PDB 1KD1.Struktur Δ6-anhidroeritromisin-A, eritronolid-A and 6-deoksieritro-misin-A dibuat melalui modifikasi struktur eritromisin-A dan dioptimasi dengan metode ab initio. Pemodelan interaksi molekul-molekul tersebut pada sisi pengikatan eritromisin-A pada rRNA 23S D.radiodurans (kristalografi sinar-X) dilakukan menggunakan metode docking molekul. Docking seluruh molekul dilakukan sebanyak sepuluh kali menggunakan program AutoDock versi 4.0 pada sisi pengikatan eritromisin-A di dalam rRNA 23S D. radiodurans dengan metode pencarian Lamarckian Genetic Algoritm. Berdasarkan hasil docking molekul, eritromisin-A, klaritromisin, roksitromisin, 6-deoksieritromisin-A, Δ6-anhidroeritromisin-A, MFE dan MMFE menempati suatu celah pada pada rRNA 23S yang hampir sama dengan celah yang ditempati eritromisin-A secara eksperimen. Hal ini menunjukkan bahwa molekul-molekul tersebut memiliki kemampuan untuk menutup peptide exit tunnel dan menghambat pemanjangan rantai polipeptida. Sementara itu, posisi pengikatan eritronolid-A, spiramisin dan kloramfenikol pada rRNA 23S berbeda dengan posisi eritromisin-A secara eksperimen. Hal ini membuktikan bahwa keberadaan gugus glikon pada cincin makrolid sangat penting pada posisi pengikatan antibiotik makrolid dan mekanisme aksi spiramisin serta kloramfenikol berbeda dengan eritromisin-A. Posisi 6-deoksieritromisin-A berimpit dengan eritromisin-A dan klaritromisin, sehingga ketiadaan gugus hidroksi C-6 pada molekul eritromisin-A tidak berpengaruh pada pengikatannya dengan rRNA 23S dan keberadaan gugus ini tidak berperan pada aktifitas antibiotik makrolid. Posisi pengikatan Δ6-anhidroeritromisin-A, MFE dan MMFE sedikit berbeda dari posisi eksperimental eritromisin-A pada celah yang sama, sehingga molekul-molekul tersebut diperkirakan memiliki kemiripan mekanisme aksi dengan eritromisin-A. Berdasarkan data energi bebas pengikatan, MMFE merupakan molekul yang terikat paling kuat pada rRNA 23S, diikuti oleh Δ6-anhidroeritromisin-A dan MFE. Kekuatan pengikatan Δ6-anhidroeritromisin-A lebih besar daripada eritromisin-A, sedangkan kekuatan MFE hampir sama dengan eritromisin-A. Dengan demikian dapat diprediksi bahwa MMFE merupakan turunan baru eritromisin yang memiliki potensi antibiotic tertinggi. Potensi antibiotik MMFE dan Δ6-anhidroeritromisin-A diprediksi lebih baik daripada eritromisin-A, sedangkan potensi MFE hampir sama dengan eritromisin-A

An interaction modeling of three new derivatives of erythromycin (Δ6-Anhydroerythromycin-A, 3-O-micarocyl-5-O-forosaminyleritronolid-B (MFE) and 3-Omicarocylmicaminocyl-5-O-forosaminyleritronolid-B (MMFE)) to 23S rRNA of Deinococcus radiodurans was conducted to to predict their antibiotic potencies. The Δ6-Anhydroerythromycin-A was synthesized using biosynthetic engineering technique and both of MFE and MMFE were synthesized using hybrid biosynthetic technique. Interaction modeling of erythromycin-A, chlarithromycin, roxythromycin, spiramycin and chloramphenicol, as well as erithronolide-A and 6-deoxyerytromycin-A were also conducted as comparisons. The X-ray christallographic structures of erythromycin-A, chlarythromycin, roxythromycin, and chloramphenicol were obtained from complex structures of these molecules to 23S rRNA Deinococcus radiodurans in Protein Data Bank situs with PDB ID : 1JZX and the structure of spiramycin was obtained from PDB ID 1KD1. The structures of Δ6 anhydroerythromycin-A, MFE, MMFE, erythronolide-A and 6- deoxyerythromycin-A were made by modification of erythomycin-A structure and optimalized with ab initio method. The interactions of these molecules to the erythromycin-A binding site of 23S rRNA of Deinococcus radiodurans which is shown by X-ray christallography were investigated using molecular docking method. The docking process of the molecules were executed ten times using AutoDock version 4.0 to the binding site of erythromycin- A to 23S rRNA of D. radiodurans by Lamarckian Genetic Algoritm as the searching method. The molecular docking method showed that erythromycin-A, chlarythromycin, roxythromycin, 6-deoxyerythromycin-A, Δ6-anhydroerythromycin-A, MFE and MMFE occupy a cavity in rRNA 23S which is similar to that occupied by erythromycin-A experimentally using X-ray christallography. It means that the studied molecules have similar capability to that of erythromycin-A in closing peptide exit tunnel and inhibiting the elongation of oligopeptide synthesis. Whilst the binding position of erithronolide-A, spiramycin and chloramphenicol in 23S rRNA are different to the experimental binding position of erythromycin-A. It is an evidence that existence of glycons in macrolide ring are very important in determining the binding position of macrolide antibiotics and the mechanism of action of kloramfenikol and spiramycin is different to erythromycin-A.The binding position of 6-deoxyerythromycin-A is overlapping to that erythromycin-A and chlarythromycin, meaning that the inexistence of the C-6 hydroxyl of erythromycin- A does not affect the binding capabilities to 23S rRNA, and the presence of this group has no pharmacological properties of macrolide antibiotic. The binding position of Δ6-anhydroerythromycin-A, MFE and MMFE is slightly different from that of experimental erythromycin-A in the same cavity, so these molecules are predicted to have similar mechanism of action to that of erythromycin-A. Based on the estimated of binding free energy, MMFE have the strongest binding capacity, followed by subsequently Δ6-anhydroerythromycin-A and MFE. The binding capacity of Δ6-anhydroerythromycin-A is stronger than erythromycin-A but MFE and erythromycin-A are similar. It could be predicted that MMFE is the new derivative of erythromycin which has the highest potency. The molecules of MMFE and Δ6- anhydroerythromycin-A are predicted have higher potency than of erythromycin-A but the potency of MFE and erythromycin-A are similar.

Kata Kunci : Pemodelan molekul,Interaksi antibiotik-rRNA 23S,MFE,MMFE,Prediksi potensi antibiotik,Molecular modeling, antibiotics-23S rRNA interaction, Δ6-anhydroerythromycin- A, MFE and MMFE, prediction of antibiotic potency