Studi Hubungan Kuantitatif Struktur-Aktivitas, Fitur Farmakofor, dan Docking Molekuler Senyawa Turunan Pirazolo-[3,4-d]-pirimidin sebagai Inhibitor Mer Tirosin Kinase

Mer Tirosin Kinase diekspresikan secara ektopik dalam sel T dan B pasien Leukemia Limfoblastik Akut (LLA), tetapi tidak diekspresikan pada sel T dan B manusia normal pada setiap tahap perkembangannya. Oleh karena itu, Mer Tirosin Kinase dapat menjadi target pengobatan LLA dengan selektifitas yang baik. Penghambatan fosforilasi reseptor Mer oleh suatu inhibitor tranduksi sinyal dapat menurunkan proliferasi sel dan meningkatkan apoptosis, sehingga menekan perkembangan sel leukemia. Pirazolo-[3,4-d]-pirimidin adalah obat generasi baru yang bertindak sebagai inhibitor dari Mer Tirosin Kinase. Tujuan penelitian ini adalah untuk menentukan deskriptor yang berpengaruh terhadap aktivitas penghambatan reseptor Mer Tirosin Kinase, menentukan fitur farmakofor ligan dan reseptor yang penting pada pengikatan ligan reseptor dan mempelajari model dan nilai energi bebas interaksi pirazolo-[3,4-d]-pirimidin dengan Mer. Pemodelan dan optimasi geometri menggunakan perangkat lunak HyperChem®. Struktur molekul optimasi geometri menggunakan metode Ab initio. Nilai prediktor dihitung menggunakan MOE® dan perhitungan statistik untuk menyusun persamaan HKSA menggunakan SPSS®. Persamaan terpilih ditentukan dengan kriteria statistik terbaik, yaitu r2, korelasi pearson, dan q2 validasi Leave One Out. Penentuan fitur farmakofor menggunakan 'Pharmacophore Query Editor' dalam perangkat lunak MOE, dengan menggunakan model senyawa hasil optimasi. Studi Docking Molekuler menggunakan 'Simulations Dock' dimana nilai scoring dihitung menggunakan pendekatan London dG. Deskriptor yang paling berperan penting berturut-turut yaitu mr, vdw vol, ASA_H, log S dan Energi LUMO. Fitur farmakofor ligan tersusun atas satu donor proton, satu akseptor proton, satu kation dan donor proton, dan satu aromatik. Jarak fitur kation dan donor proton dengan aromatic (6.92 Ǻ) penting untuk dipertahankan sebagai inhibitor Mer. Fitur farmakofor reseptor tersusun atas satu akseptor proton (Met 674), tiga donor proton (Pro 672, Arg 727 dan Asn 728) dan satu anion (Asp 678), yang penting dalam pengikatan dengan fitur farmakofor ligan. Seluruh senyawa turunan pirazolo-[3,4-d]-pirimidin memiliki skoring yang baik dimana senyawa 40 memiliki nilai terbaik yaitu -12.7584 kkal/mol.Kata kunci: leukemia limfoblastik akut, pirazolo-[3,4-d]-pirimidin, Mer, HKSA, fitur farmakofor.AbstractMer Tyrosine Kinase is ectopically expressed in T and B cells of Acute Lymphoblastic Leukemia (ALL) patient, but is not expressed innormal human T and B cells at any stage of its development. Therefore Mer Tyrosine Kinase can be a treatment target al.L with a good selectivity. Phosphorylation inhibition of Mer receptor by signal transduction inhibitor decreases cell proliferation and increases apoptosis, there by suppressing the development of leukemia cells. Pirazolo-[3,4-d]-pyrimidines area new generation of drugs that act as inhibitors of Mer Tyrosine Kinase. The purposes of the presentre search are to determine descriptors that influence the inhibitory activity on Mer receptor Tyrosine Kinase, to determine the ligands pharmacopores features and receptors which play important roles in ligand-receptors binding and to study model and free energy value of pirazolo-[3,4-d]-pyrimidines with Mer interactions. Modeling and optimization geometry was carried out using HyperChem® software. Molecules structure were geometrically optimized using Ab initio method. Predictors values were computed using MOE® and statistical calculations of QSAR equations was carried out using SPSS®. The selected equation was determined by the best statistical criteria, such as r2, Pearsoncor relations, and q2 Leave One Out validation. Determination of pharmacophores features used optimized model structure using 'Pharmacophore Query Editor' in the MOE software. The study Moleculard ocking used 'Simulations Dock' where the scoring values were calculated using the Londond Gapproach. The most important descriptors were mr, volvdw, ASA_H, logS and LUMO energy. Ligands pharmacophores features were composed of aproton donor, aproton acceptor, one cations and proton donors, and aromatic. Distance (6.92 Ǻ) between cation and proton donors features with aromatic group play important role as Mer inhibitors. Receptor pharmocophore features were composed of aproton acceptor (Met 674), three proton donors (Pro 672, Arg727 and Asn728) and one anion (Asp 678), which is important in the binding with ligand features pharmacopore. All of pirazolo-[3,4-d]-pyrimidines derivates had good docking score where as compound 40 had the best scoring -12.7584 kcal/mol.Keywords: acute lymphoblastic leukemia, pyrazolo-[3,4-d]-pyrimidine, Mer, QSAR, pharmacophore feature

Hubungan Kuantitatif Struktur dan Aktivitas Senyawa Turunan 3-Haloasilaminobenzoilurea sebagai Inhibitor Pembentukan Mikrotubulus

Mikrotubulus (MTα) telah diidentifikasi sebagai tempat kerja untuk pengobatan kanker dalam penghambatan pembelahan sel. Salah satu senyawa yang memiliki potensi antikanker yang bekerja pada situs ini adalah turunan 3-haloasilamino benzoilurea. Mekanisme kerja senyawa ini yaitu berikatan pada daerah colchicine binding site pada β-tubulin, dimana akan mengganggu pembentukan benang-benang mitotik mikrotubulus, memblokade siklus sel pada fase mitosis, yang berdampak pada apoptosis sel kanker. Penelitian ini bertujuan untuk memperoleh persamaan Hubungan Kuantitatif Struktur dan Aktivitas (HKSA) terbaik, senyawa-senyawa baru yang memiliki aktivitas antikanker lebih tinggi dan afinitas yang lebih baik terhadap reseptor β-tubulin, dibandingkan dengan senyawa induknya. Dilakukan pemodelan dan optimasi geometri menggunakan Hyperchem. Selanjutnya dilakukan perhitungan nilai prediktor diikuti analisis statistik multilinear masing-masing menggunakan MOE 2007.09 dan SPSS Statistic 17.0 dan analisisnya divalidasi dengan metode Leave One Out. Setelah mendapatkan persamaan HKSA yang terbaik, dilakukan desain senyawa baru menurut skema Topliss. Derivat senyawa baru kemudian didocking pada reseptor β-tubulin untuk melihat afitinasnya terhadap reseptor. Persamaan HKSA terbaik untuk senyawa turunan 3-haloasilamino benzoilurea adalah IC50 = "’15,077 (± 1,996) "’ 0,160 (±0,055) AM1_dipole + 0,016 (±0,004) AM1_HF + 0,521 (±0,250) AM1_LUMO + 0,038 (±0,005) ASA_H dengan 3 senyawa baru yang memiliki IC50 lebih rendah daripada senyawainduk.Kata kunci: kanker, benzoilurea, HKSA, docking, mikrotubulus. Microtubules (MTα) has been identified as a rational site to inhibit the dividing of cancer cells in cancer therapy. One of theanticancer compounds that work at this site is 3-haloacylamino benzoylurea derivatives. The mechanism of this compound is to bind with the region of cochicine binding site at the β-tubules, which interferes the assembly of mitotic spindles of microtubules, followed by blocking the cell cycle at mitotic phase then caused the apoptosis of cancer cell. The present study is aimed to obtain the best Quantitative Structure and Activity Relationship (QSAR) equation of 3-haloacylamino benzoylurea derivatives, design its new derivatives that have a higher anticancer activity and higher affinity towards the β-tubulin receptor than its parent compound. Structure modeling and geometric optimization structure, were done by Hyperchem. The calculation of predictors' value was performed by MOE 2007.09, while multilinear statistical analysis was done with SPSS Statistic 17.0. The results were then validated by Leave One Out method. After the best QSAR equation has been obtained, the new derivatives were designed according to the Topliss scheme. New compounds were docked to the β-tubulin receptor to observe the binding affinity and energy. It was obtained that the best QSAR equation is IC50 = "’15.077 (± 1.996) "’ 0.160 (±0.055) AM1_dipole + 0.016 (±0.004) AM1_HF + 0.521 (±0.250) AM1_LUMO + 0.038 (±0.005) ASA_H. 3 new derivatives have the IC50 lower than the parent compound.Keywords: cancer, benzoylurea, QSAR, docking, mircrotubules

HOMOLOGY MODELING EPITOP ISOCITRATE DEHYDROGENASE TIPE 1 (R132H) MENGGUNAKAN MODELLER, I-TASSER DAN (PS)2 UNTUK VAKSIN GLIOMA

Glioma merupakan jenis tumor otak ganas primer. Adanya glioma dapat ditandai dengan mutasi R132H pada Isocitrate dehydrogenase tipe 1 (IDH1). IDH1 (R132H) yang mengandung epitop imunogenik yang spesifik terhadap tumor dan cocok untuk dijadikan vaksin perlu diketahui strukturnya. Oleh karena itu, perlu dilakukan homology modeling epitop IDH1 (R132H). TMHMM, MEMSAT-SVM dan MEMSAT3 digunakan untuk memprediksi topologi transmembran IDH1 (R132H). Analisis epitop-epitop IDH1 (R132H) dilakukan menggunakan NetMHCII dan IEDB. Epitop-epitop hasil analisis diprediksi antigenisitasnya dengan menggunakan VaxiJen sehingga didapatkan 91 epitop. Homology modeling epitop-epitop yang memiliki kemungkinan sebagai antigen dilakukan dengan menggunakan Modeller, I-TASSER dan (PS)2. Hasil homology modeling epitopepitop IDH1 (R132H) divalidasi dengan MolProbity, ProSA-web dan QMEAN. Kemudian dipilih satu model 3D dari tiga model hasil homology modeling untuk setiap epitop dan dilakukan refinement pada struktur Epitop-1 sampai Epitop-91 dengan menggunakan GalaxyRefine dan GROMACS untuk minimisasi energi

Pharmacophore Modeling, Docking, and Molecular Dynamics Simulation of Flavonoids as Inhibitors of Urokinase-type Plasminogen Activator

The urokinase-type plasminogen activator (uPA) system plays a significant role in the invasion and metastasis of cancer cells. The present study was conducted to investigate natural product compounds as inhibitors and hit molecules of uPA using in-silico analysis. A pharmacophore model was built to screen the Indonesian Herbal Database (HerbalDB) to obtain inhibitors of different scaffolds. Based on the molecular docking score, four ligands were selected as potential uPA inhibitors. Subsequently, the stability of the ligand-uPA complex was analyzed using molecular dynamics (MD) simulation. An RMSD graph of the backbone protein and the RMSF values of the amino acid residues were also determined. In addition, the MM-PBSA method was applied to calculate the free binding energy. According to the results, Model_3, characterized by aromatic rings 23 (F1 and F2), cationic H-bond donor (F3), and metal ligator (F4) features, had an adequate goodness-of-hit score (GH). The four top-ranked ligands, isorhamnetin, rhamnetin, quercetin, and kaempferol, showed higher docking scores compared to the others. This study confirmed that isorhamnetin, rhamnetin, and kaempferol build stable complexes with uPA with lower binding energy than quercetin

Pharmacophore Modeling, Docking, and Molecular Dynamics Simulation of Flavonoids as Inhibitors of Urokinase-type Plasminogen Activator

The urokinase-type plasminogen activator (uPA) system plays a significant role in the invasion and metastasis of cancer cells. The present study was conducted to investigate natural product compounds as inhibitors and hit molecules of uPA using in-silico analysis. A pharmacophore model was built to screen the Indonesian Herbal Database (HerbalDB) to obtain inhibitors of different scaffolds. Based on the molecular docking score, four ligands were selected as potential uPA inhibitors. Subsequently, the stability of the ligand-uPA complex was analyzed using molecular dynamics (MD) simulation. An RMSD graph of the backbone protein and the RMSF values of the amino acid residues were also determined. In addition, the MM-PBSA method was applied to calculate the free binding energy. According to the results, Model_3, characterized by aromatic rings 23 (F1 and F2), cationic H-bond donor (F3), and metal ligator (F4) features, had an adequate goodness-of-hit score (GH). The four top-ranked ligands, isorhamnetin, rhamnetin, quercetin, and kaempferol, showed higher docking scores compared to the others. This study confirmed that isorhamnetin, rhamnetin, and kaempferol build stable complexes with uPA with lower binding energy than quercetin

Formulasi Mikroemulsi Glukosamin Hidroklorida

Glukosamin hidroklorida (glukosamin HCl) merupakan senyawa yang sudah populer sebagai suplemen untuk mengurangi rasa nyeri dan kerusakan sendi pada penderita osteoarthritis. Namun terdapat beberapa faktor yang menjadi tantangan dalam pengembangan sediaan glukosamin, yaitu dosis yang besar untuk diabsorpsi secara perkutan serta masalah stabilitas glukosamin di dalam air yang mudah sekali membentuk maillard product. Penelitian ini bertujuan untuk mengembangkan mikroemulsi glukosamin HCl untuk penggunaan transdermal sehingga permeabilitas terhadap stratum korneum meningkat dan stabilitas sediaan lebih baik. Dalam penelitian ini glukosamin HCl dikembangkan dalam bentuk mikroemulsi M/A dan diperoleh formula optimum dengan komposisi glukosamin HCl 15%, isopropil miristat 4,2%, Tween 80 22,70%, isopropil alkohol 5,70%, natrium metabisulfit 0,10%, aquadeion 52,30%. Uji karakterisasi menunjukkan mikroemulsi memenuhi persyaratan secara organoleptis, viskositas, serta ukuran globul. Mikroemulsi stabil pada uji sentrifugasi. Sementara uji kadar dengan menggunakan metode KCKT diperoleh hasil 14,9%

Computational Study of Nocardiotide-A Analogues in the Development of Technetium-99m Radiopeptides for Cancer Imaging for Targeting Somatostatin Receptor 2

Nocardiotide-A (cWIWLVA) is a cyclic peptide with significant cytotoxicity against several cancer cells. The present research aimed to design a radiopeptide based on nocardiotide-A analogues to be labeled by technetium-99m targeting SSTR2, which is the most widely expressed receptor in several types of human cancers and used as radiopeptide target. Nocardiotide-A analogues were individually designed by replacing valine at the lead compound with lysine, arginine, histidine, asparagine, and glutamine, and this was simulated by molecular dynamics using AMBER18. A molecular docking using AutoDock 4.2 was performed and evaluated to understand the effect of chelation of technetium-99m on 99mTc-HYNIC-EDDA and 99mTc-HYNIC-tricine on the binding affinity of nocardiotide-A analogues. The molecular dynamics simulation confirmed that the designed nocardiotide-A-based peptides were stable in the binding pocket of SSTR2 for 200 ns. Moreover, the nocardiotide-A-based radiopeptides are able to interact with residues Q102, D122, Q126, and N276 by building hydrogen bonds, which are essential binding residues in SSTR2. The molecular docking simulation revealed that the best docking parameter is exhibited by 99mTc/EDDA/HYNIC-cWIWLNA and 99mTc/tricine/HYNIC-cWIWLNA with a binding free energy of –12.59 kcal/mol and –8.96 kcal/mol, respectively. Taken together, nocardiotide-A-based radiopeptides are prospective to be further developed for cancer imaging targeting SSTR2

ELECTRONIC ABSORPTION SPECTRA OF SOME PHOTOSENSITIZERS BEARING CARBOXYLIC ACID GROUPS: INSIGHTS FROM THEORY

Objective: The main objective of this research work was to give insight from theory in interpreting electronic absorption spectra of tetrapyrrolic macrocycles bearing carboxylic acid groups: protoporphyrin IX, pheophorbide a and its 1-hydroxyethyl derivatives for application in photodynamic therapy.Methods: All calculations were carried out by using the Gaussian 03W version 6.0. Electronic excitation energies and oscillator strengths were computed as vertical excitations from the minima of the ground state structures by using ZINDO and TD-DFT approach in vacuo. The simulated spectra were obtained by using the GaussSum 2.2.0 program.Results: The results showed that chlorine compounds (pheophorbide a and its 1-hydroxyethyl derivative) display the red-most absorption (Qx) at longer wavelengths and their absorption were stronger than porphyrin compounds (protoporphyrin IX and its 1-hydroxyethyl derivative). On the other hand, the 1-hydroxyethyl derivatives were not able to red-shift the absorption compared to the parent compounds.Conclusion: The chlorin compounds bearing carboxylic acid groups were, however, more promising candidates to be utilized in PDT compared to the corresponding porphyrin compounds.Keywords: Absorption spectra, 1-Hydroxyethyl derivative, Photodynamic therapy, Pheophorbide a, Protoporphyrin IX, TD-DFT, ZIND

Computational Study of Nocardiotide-A Analogues in the Development of Technetium-99m Radiopeptides for Cancer Imaging for Targeting Somatostatin Receptor 2

Nocardiotide-A (cWIWLVA) is a cyclic peptide with significant cytotoxicity against several cancer cells. The present research aimed to design a radiopeptide based on nocardiotide-A analogues to be labeled by technetium-99m targeting SSTR2, which is the most widely expressed receptor in several types of human cancers and used as radiopeptide target. Nocardiotide-A analogues were individually designed by replacing valine at the lead compound with lysine, arginine, histidine, asparagine, and glutamine, and this was simulated by molecular dynamics using AMBER18. A molecular docking using AutoDock 4.2 was performed and evaluated to understand the effect of chelation of technetium-99m on 99mTc-HYNIC-EDDA and 99mTc-HYNIC-tricine on the binding affinity of nocardiotide-A analogues. The molecular dynamics simulation confirmed that the designed nocardiotide-A-based peptides were stable in the binding pocket of SSTR2 for 200 ns. Moreover, the nocardiotide-A-based radiopeptides are able to interact with residues Q102, D122, Q126, and N276 by building hydrogen bonds, which are essential binding residues in SSTR2. The molecular docking simulation revealed that the best docking parameter is exhibited by 99mTc/EDDA/HYNIC-cWIWLNA and 99mTc/tricine/HYNIC-cWIWLNA with a binding free energy of –12.59 kcal/mol and –8.96 kcal/mol, respectively. Taken together, nocardiotide-A-based radiopeptides are prospective to be further developed for cancer imaging targeting SSTR2