Lung cancer is one of the leading causes of cancer-related deaths in the world among both men and women. Several studies in the literature report that overexpression and mutation of the epidermal growth factor receptor (EGFR) are implicated in the pathogenesis of some lung cancers. Nimotuzumab is a humanized monoclonal antibody (mAb) that inhibits EGF binding because it binds to the extracellular domain of the EGFR. Nimotuzumab requires bivalent binding for stable attachment to cellular surface, which leads to nimotuzumab selectively binding to cells that express mAbs of moderate to high EGFR levels, and this could explain its low toxicity. This property has an advantage for development of nimotuzumab as a therapeutic and diagnostic agent. Monoclonal antibodies are large in size (150 kDa), thus penetrating slowly and residing in the blood for extended periods of time (from days to weeks); their use in imaging studies can result in low signal-to-background ratios and poor image quality. A reduction in the size of the immunoglobulin molecule has also been proposed as a means for increasing tumor penetration by mAbs. Nevertheless, it is known that the penetration of mAb into tumor cell is slow, due to its high molecular weight. Therefore, mAb is not very attractive to be used for imaging diagnostic purpose because of its kinetics and potential to elicit antibody response. The objective of this research was to study the homology modeling of a simpler functional molecule based on nimotuzumab, which consists of 2 antigen-binding fragments (Fab), namely, F(ab′)2, using MODELER. The crystal structure of Fab of nimotuzumab from protein data bank was used as a template to construct the model of F(ab′)2. Molecular dynamic simulation was performed to evaluate the stability of F(ab′)2 and conformational changes of F(ab′)2 in simulation. The result showed the dynamic behavior of antigen-binding site region of F(ab′)2 throughout simulation. This result is expected to be useful in the further development of F(ab′)2 fragment nimotuzumab as a lung cancer diagnostic.

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ancer is one of the major health problems in the world. Early detection using Magnetic Resonance Imaging (MRI) for the presence of cancer cells could improve the successful rate of treatment. For this reason, a selective contrast agent is required to improve the accuracy of cancer diagnosis. Many cancer cells overexpress the folate receptor alpha (FRA) on its surface. Therefore, the substrate of FRA, folic acid, can be used to develop a selective contrast agent such as Gd-DTPA-folate. However, it is worth noting that the slightly acidic pH in cancer cell could change the conformation of ligand binding site of FRA, thus lowering the affinity of folic acid-based contrast agent. Although the crystal structure of FRA in low pH has been solved, but the mechanism of decreasing affinity of folic acid is still not clear. Therefore, this work aims to study the structural change of FRA in low pH and to investigate the molecular interactions of folic acid and Gd-DTPAfolate to the FRA at normal and acidic pH using molecular dynamics simulations.A crystal structure of folic acid in complex with FRA was used as a template for simulations. The interaction energies were calculated using MM/GBSA method. As a result, the protonated Asp81 in the ligand binding site of FRA repulsed the pterin ring of folic acid. Interestingly, Gd-DTPA-folate was predicted to stabilize its interaction with FRA in low-pH as compared to the normal pH. It is hoped that this study could provide insight into the development of selective contrast agent for cancer.

Gadolinium dietilentriaminpentaasetat-folat (Gd-DTPA-Folat) telah diusulkan sebagai senyawa pengontras magnetic resonance imaging yang memiliki potensi diagnosis penyakit kanker yang mengekpresikan reseptor folat berlebih. Pada studi sebelumnya, DTPA-Folat sebagai ligan pengompleks dari Gd-DTPA-Folat disintesis melalui pembentukan derivat asam folat, etilendiamin-folat (EDA-Folat) melalui lima tahapan reaksi. Pada studi ini, metode sintesis dari derivat asam folat, EDA-Folat menggunakan metode sintesis secara tidak langsung (sintesis (γ)EDA-Folat) akan dibandingkan dengan metode sintesis secara langsung (sintesis (α)EDA-Folat dan (γ)EDA-Folat). Asam folat akan dikonjugasikan dengan N-hidrosuksisuksinimida (NHS) untuk membentuk NHS-Folat, selanjutnya dikonjugasikan dengan EDA akan menghasilkan EDA-Folat. EDA-Folat yang dihasilkan akan dikarakterisasi dengan spektrotrofotometri UV, inframerah dan spektroskopi massa. Analisis kemurnian dari produk EDA-Folat yang dihasilkan akan diuji dengan KCKT kolom C18, fase gerak asetonitril/air (TFA 0,5%) 2:8, laju alir 0,5 mL menit dan detektor UV-DAD 280 nm, uji statistik menggunakan software minitab 15 dilakukan untuk menguji perbedaan kedua metode. Perolehan hasil menunjukkan karakteristik yang identik antara produk EDA-Folat yang disintesis secara langsung dan tidak langsung dengan spektrotrofotometri UV, inframerah dan spektroskopi massa. Uji statistik dengan software minitab 15 menunjukkan bahwa tidak ada perbedaan antara kedua metode sintesis EDA-Folat.

Objective: Despite the availability of the commercial rapid tests of chikungunya, the difference of pathogen's genotypes amongst different countries has created some causes for concern. It is found that the sensitivity of the current chikungunya rapid tests on Asian strain was only 20.5%, as compared to 90.3% when tested on the African phylogroup. Therefore, the development of diagnostics that is specific for the current strain circulating in the country is important to be done. The cryo-electron microscopy (cryo-EM) structures of antigen-antibody complex can be used as an insightful structural basis to the development of the tailored antibody for diagnostics purposes. However, cryo-EM structures usually were resolved in low resolution, thus some sterical clashes between residues are expected. This work aims to refine the cryo-EM structures of E1-E2 of chikungunya virus in complex with antibody using molecular mechanics method, to calculate the binding energy of antigen-antibody complex, and to compare it with the experimental results. Methods:The cryo-EM structures were refined in vacuo by short minimization scheme using AMBER 14. The binding energies were calculated using FireDock and Molecular Mechanics Generalized Boltzmann Surface Area methods. Results:The results showed that the direct calculation of binding energies of cryo-EM structures reflected high repulsive forces. While the calculation on the refined structure showed lower binding energies. Visual inspections on the complex structures also indicated that the refined structures showed better interactions. Conclusion:The refinement of cryo-EM structures should be useful to gain more insight into the binding mode of interactions between antigenic protein and antibody, at the atomic level.