STUDI IN SILICO INTERAKSI BEBERAPA KATIONIK PORFIRIN DENGAN UNTAI GANDA DNA

• Main Author: Arifian S Farm, Hanggara
• Format: Theses
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/79017
• Institution: Institut Teknologi Bandung

Background and purpose : The interaction of the porphyrin and its derivatives with DNA has become the attention of researchers since decades ago. Ability of porphyrin to bind to the DNA strand and its sensitivity to light makes phorphyrin has been intensively developed as a photosensitizer agent for cancer therapy. The present research aims to explore the interaction of some porphyrin derivatives to double stranded DNA in silico. Method and results : Porphyrin’s model compounds were constructed using HyperChem 8.0.10 package and were then geometry optimized using ab initio methods. Minimum energy of each compounds were analyzed using the Molecular Operating Environment (MOE) 2009.10. Docking simulation is then performed for each compound against doublestranded DNA. Molecular dynamics simulations were conducted to the DNAporphyrin complex which have RSMD value less than 2.0. All docking and molecular dynamics simulations were performed using Molecular Operating Environment (MOE) 2009.10. Geometry optimization results indicated that TDM-2-IMP4+ (4Cl-) has the lowest energy i.e. –222.79 (x 103 kCal / mol). While docking simulation showed that DNA+TM-4-PyP4+ has the best affinity to DNA (– 27.01 kCal / mol). Molecular dynamics simulation for 5 picoseconds showed that complex of DNA+TDM-2-ImP4+ have the lowest levels of potential energy, i.e. – 656.96 kCal / mol, while the kinetic energy of DNA+TDM-2-ImP4+ complex have the minimum energy of 321.32 kCal / mol. Molecular dynamics simulation showed that complex of DNA+TDM-2-ImP4+ have the lowest energy of –335.64 kCal / mol. Conclusion : All porphyrins bind to DNA in major groove. Based on the molecular dynamics simulations in terms of potential energy ratio, kinetic energy and total energy, interaction of TDM-2-ImP4+ with double-stranded DNA can produce a stable interaction.