Established in November 2022 within the Istanbul Technical University Technopark, PeptiSyn provides innovative biotechnology services. Launched with a start-up grant from the TUBITAK-1512 programme, the company specializes in the production of peptides on both large and small scales. These peptides have broad applications in biomedical, medical, chemical, and cosmetic fields, among others. PeptiSyn focuses on the design of peptides using in silico methods and their synthesis through solid or solution-based techniques.
Technical/Scientific Challenge
Human immunodeficiency virus infection and acquired immunodeficiency syndrome (HIV/AIDS) are a spectrum of conditions caused by infection with the human immunodeficiency virus (HIV), a retrovirus. During this disease, the immune system gradually breaks down, allowing life-threatening opportunistic infections to thrive.
Upon diagnosis, the patient immediately begins antiretroviral therapy (ART). However, despite ART, the immune system can lose its ability to clear pathogens from the body, leading to potentially fatal opportunistic infections. To fully restore the immune system, HIV Tat protein should be targeted. This protein has several detrimental effects, including the inhibition of phagocytosis in macrophages. For this reason, we propose developing a PROTAC for the Tat protein using in silico methods to knock down this protein in infected cells. This will generate a novel therapeutic aiming to restore the immune system during HIV infection.
Solution
As we failed to yield PROTACs with free servers and related tools, we decided to construct them manually by merging individual protein-ligand complexes. To this respect, 15 PROTAC structures were created by changing the linker molecule, and simulation files for these structures were prepared. Subsequently, 1000 ns MD simulations of these structures were carried out, and 5 of these simulations were completed and are currently analysed.
MD simulations were performed with Desmond simulation package. Simulation systems contain approximately 90K atoms. Simulations were performed at 298K and 1 atm conditions. SPC water model and OPLS2005 force-field are used in the simulations. Atomic coordinates were recorded with 20ps intervals. 9 Å cut-off distance is applied. Nosé–Hoover thermostat and the Martyna–Tobias–Klein barostat are used for temperature and pressure control. The simulation time step was 2 fs with the r-RESPA integration method utilized.
Figure 1: The overall structure of tertiary complex of PROTAC for HIV Tat.
Business Impact
As PeptiSyn, our core vision is to produce peptides, which are heavily used in the cosmetics and healthcare sectors, within our country. Although there are many academicians working in the field of peptide production in our country, the commercial production of peptides is extremely limited. In fact, there are only two companies working in the field of peptide production in Turkey.
However, one of the services we envisaged during the establishment phase of our company is the design of peptides in a computer environment. Indeed, the founder of our company, Associate Professor Dr. Onur Alpturk, collaborates with Assistant Professor Dr. Sefer Baday, the NCC of this project, in areas such as designing peptides for various purposes and examining the interactions of peptides with proteins.
This partnership and the EuroCC 2 project have enabled PeptiSyn to gain competence in areas such as molecular docking and MD simulations. Additionally, the company has gained knowledge in preparing simulation files, uploading and downloading simulation files to necessary servers, and analysing simulation files. This experience will enable PeptiSyn to become a company that not only produces peptides but also designs peptides in a computer environment in the future.
Benefits
- Hands-on experience on computational PROTAC design: The PROTAC approach, which emerged in the early 2000s, has evolved to a point where it is widely used in the degradation of many proteins or enzymes that are key to diseases, ranging from cancer to neurological diseases. As a result of the dizzying developments in this field, leading pharmaceutical companies around the world have begun to develop PROTAC-based drugs, some of which reached Phase I/Phase II trials. Therefore, the scope of this EuroCC 2 project aligns with the current state of PROTAC technology. Through this project, PeptiSyn has accumulated knowledge in designing PROTACs through in silico methods, which is of great importance in pharmaceutical and medicinal chemistry. Upon the completion of this project, PeptiSyn has now the potential to provide consultancy services to pharmaceutical companies and offer the design of such molecules as a service when needed.
- Pharmaceuticals: Thanks to the development of effective antiviral drugs, HIV/AIDS, which emerged as a fatal disease in the 1980s, has become a manageable chronic condition today. The antiretroviral therapy developed in the early 1990s has saved millions of lives, preventing the progression of HIV infection to AIDS by inhibiting viral replication and increasing CD4+ T cell counts. Recent efforts have focused on developing new approaches to strengthen antiretroviral therapy, targeting virulence proteins such as Tat. However, antiviral therapy cannot fully suppress the release of the Tat protein, which plays a crucial role in the collapse of the immune system. Additionally, it is known that diseases capable of developing an anti-Tat immune response generally progress more slowly and that antiretroviral therapy is more effective in these cases. These findings clearly demonstrate the significance of Tat protein as a therapeutic target.
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Developing a treatment for HIV/AIDS using Tat inhibitors, which are of great importance in HIV pathogenesis and replication, is feasible. In the “block and lock” approach, Tat inhibitors can block viral replication, thereby preventing virus proliferation and reducing viral reservoirs. Studies on Didehydro-cortistatin A have shown that this compound binds to the Simian Immunodeficiency Virus (SIV) Tat protein, inhibiting the Tat-TAR interaction and halting chronic/acute SIV infection at nanomolar levels. Thus, developing molecules that can inhibit the effects of the Tat protein within cells is critical for the ultimate treatment of HIV. From this perspective, PROTACs designed for the Tat protein represent a new approach that could enhance the efficacy of antiviral therapy used in treating HIV in the future.
Keywords
HPC, MD simulations, PROTAC, Tat protein, HIV/AIDS
Contact:
Onur Alpturk: onur.alpturk@itu.edu.tr
Prof. Sefer Baday: badays@itu.edu.tr
