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Ms. Madhmita Aggunna

(Ex-Faculty of TCABS-E)

B.Tech. (Biotechnology)

Currently pursuing...M.S. (Experimetal Medicine)

 

Drug Discovery using CADD

Multiomics-Oncology & Immunotherapy Branch, 

Department of Intramural Research Core (IRC)

The Center for Advanced-Applied Biological Sciences & Entrepreneurship (TCABS-E), Visakhapatnam (A.P.) India.

​​Telephone: +91 8660301662; Email: aggunnamadhumita(at)gmail(dot)com.

NIH Biosketch coming soon...

Research Interests:

Drug Discovery: Helicobacter pylori infections.

Helicobacter pylori is a Gram negative bacterium that is capable of surviving in the acidic environment of the human stomach by releasing the Urease enzyme to neutralize the local acidity. H. pylori is responsible for majority of gastric ulcers and 75% of the gastric cancers worldwide. Cytotoxin-associated gene A (CagA) protein is one of the virulence factors that is injected into the gastric epithelial cells through the bacterial T4SS mechanism. We performed a virtual screening of a focused library containing 30 structurally diverse compounds from the ZINC database using H. pylori CagA protein taken from the X-ray crystal structure, PDB ID:4IRV as the drug target. The ASPP2 binding pocket in CagA was used for docking the compounds using SwissDock. Among the 30 compounds in the library, we identified a hit molecule, MA01027 with the highest binding affinity (Patent No. 202441101766). MA01027 was further synthesized and evaluated in vitro for its antibacterial activity using clinical patient gastric biopsy-derived H. pylori bacteria. The H. pylori isolates were characterized and a set of four standard antibiotics were used along with MA01027 for the in vitro antibacterial activity evaluation. MA01027 exhibited >90% inhibition of bacterial growth and is currently going through in vivo studies.​​​

Applications of multiomics to Oncology & Immunotherapy.

According to the International Agency for Research on Cancer (IARC), the number of cancer patients rose to 17.0 million and there are 9.5 million deaths due to cancer worldwide. The immune system is a complex network of defense mechanisms against foreign bodies and also terminally differentiated cancer cells. The immune system can distinguish foreign bodies and cancer cells from healthy cells except in the tumor microenvironment (TME). Cancer-Immunotherapy (Can-IT) is a biologics-based therapy for the treatment of diseases by modulating the immune system. Can-IT is an excellent synergistic approach along with chemotherapy either with/without radiation. Failure in patient response to Can-IT has been a challenging medical task to date. Although different research groups have evaluated various reasons for the failure of Can-IT, we believe that more accuracy can be achieved by using a multi-omics approach for a deeper investigation and analysis. Thus, we propose an Immunomics-based approach that considers multi-omics for the evaluation of patient’s immune system in the context of Can-IT.

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Patents​

  • Aggunna, M. and Yedidi, R.S. (2021). Proteolysis targeting chimera based composition for gastritis and gastric ulcers. Patent No. 202141058294.

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  • Vissapragada, M., Aggunna, M. and Yedidi, R.S. (2023). A probiotic vaccine for preventing coronavirus infection and preparation method. Patent No. 202341008573.

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  • Aggunna, M. and Yedidi, R.S. (2024). Antibacterial application of pyrrolidin-piperdine derivatives containing composition to inhibit Helicobacter pylori replication, preparation method thereof. Patent No. 202441101766.

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  • Venkat, P., Aggunna, M. and Yedidi, R.S. (2025). Microwave-assisted synthesis of 4-(pyrrolidin-1-yl)-piperidine and derivatives following green chemistry principles. Patent No. Awaiting...

Publications (Listed Chronologically)

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  1. Aggunna, M., Yedidi, R.S. (2020) The OMICAS, Can-IT: Onco-Molecular Immunotherapeutic Constellation Analytics Spectrum in Cancer Immunotherapy. TCABSE-J, Spl. issue 1:24-26. Epub: Oct 25th , 2020.            (View publication)​

  2. Aggunna, M., Yedidi, R.S. (2021) Circos plot: a colourful depiction of highly knotty and convoluted scientific data. TCABSE-J, Vol. 1, Issue 2:33-34. Epub: Oct 15th, 2021. (View publication)​

  3. Aggunna, M., Yedidi, R.S. (2021) HelicoTAC©, a PROTAC-based small molecule targeting the virulence factor Cag A of H. pylori as a potential therapeutic for gastritis and gastric cancers. TCABSE-J, Vol. 1, Issue 3:46-48. Epub: Apr 2nd, 2022. (View publication)

  4. Aggunna, M., Grandhi, V.K.S.A., Yedidi, R.S. (2022) Artistic representation of scientific data: prediction of mutant SARS-CoV-2 viral fitness based on the viral spike protein coding mRNA stability. TCABSE-J, Vol. 1, Issue 3:1-3. Epub: Apr 2nd, 2022. (View publication)

  5. Gampa, S., Aggunna, M., Grandhi, A.V.K.S., Adduri, V., Ayithamsetti, P., Korabu, M., Addala, S., Vissapragada, M., Palakurty, M., Yedidi, R.S.  (2022) Increase in the predicted mRNA stability of certain SARS CoV-2 mutant spike proteins compared to wild type may pose potential risk to vaccines. TCABSE-J, Vol. 1, Issue 3:4-9. Epub: Apr 2nd, 2022. (View publication)

  6. Aggunna, M., Yedidi, R.S. (2022) In silico quantitative structure-activity relationship analysis of a highly potent experimental HIV-1 protease inhibitor, GRL10413. TCABSE-J, Vol. 1, Issue 3:10-17. Epub: Apr2nd , 2022. (View publication)

  7. Addala, S., Vissapragada, M., Aggunna, M., Mukala, N., Lanka, M., Gampa, S., Sodasani, M., Chintalapati, J., Kamidi, A., Veeranna, R.P., Yedidi, R.S. (2022) Success of Current COVID-19 Vaccine Strategies vs. the Epitope Topology of SARS-CoV-2 Spike Protein-Receptor Binding Domain (RBD): A Computational Study of RBD Topology to Guide Future Vaccine Design. Vaccines. 2022; 10(6):841. https://doi.org/10.3390/vaccines10060841

  8. Maru, K., Mukala, N., Aggunna, M. and Yedidi, R.S. (2022). Evaluation of genotoxicity caused by the carcinogenic benzo[a]pyrene, a common ingredient of Indian tobacco chew, using a bacterial gene expression model. TCABSE-J, Vol. 1, Issue 4:1-8. Oct 5th, 2022. Epub: Oct 5th, 2022. (View publication)

  9. Nerusu, V.R.D., Aggunna, M. and Yedidi, R.S. (2022). Testing the feasibility of using the common laboratory strain E. coli DH5α as a model system to study clarithromycin-resistance in Helicobacter pylori. TCABSE-J, Vol. 1, Issue 4:28-34. Oct 5th, 2022. Epub: Oct 5th, 2022. (View publication)

  10. Vissapragada, M., Addala, S., Aggunna, M., Mukala, N., Chintalapati, J., Kamidi, A., Korabu, M. S., Lanka, M., Palla, H., Sodasani, M., Grandhi, A. V. K. S., Unnisa, A., Adhikari, A., Kumpatla, A. D., Yerabolu, B., Paidi, C., Pemmadi, G., Penta, H., Mallavalli, H., Gadigoyala, K., Voleti, M., Ravilisetty, M., Akula, N., Gundubogula, P., Puripanda, P., Lankapalli, P., Sandipamu, P., Nagraj, R., Tamarala, R., Geddam, R., Kolluru, R., Oggu, R., Garbhapu, R., Meka, S., Geddam, S., Viyyapu, S., Sammangi, S., Javvaji, S., Chattopadhyay, S., Inemella, S., Grandhi, V., Chigilipalli, Y., Puppala, Y. C., Sharma, M. H., Gubbala, S., Thakur, K., Aanaparthi, S., Pothula, B. and Yedidi, R.S. (2023). In silico analysis of molnupiravir usage vs. efficacy of COVID-19 vaccines. TCABSE-J, Vol. 1, Issue 5:1-14. Mar 22nd, 2023. Epub: Oct 20th, 2022. (View publication)

  11. Mukala, M., Aggunna, M., and Yedidi, R. S. (2023). Sequence homology-based identification of paracetamol metabolizing enzymes in chicken liver homogenates for in vitro drug metabolism studies. TCABSE-J, Vol. 1, Issue 5:12-19. Mar 22nd, 2023. Epub: Oct 25th, 2022. (View publication)

  12. Grandhi, A.V.K.S., Aggunna, M., and Yedidi, R. S. (2023).Solvent-guided quantitative structure-activity relationship (SG-QSAR): In silico SG-QSAR-based improvement of the human uridine phosphorylase-2 inhibitor binding affinity with potential applications in reducing the toxicity of chemotherapy. TCABSE-J, Vol. 1, Issue 5:20-25. Mar 22nd, 2023. Epub: Mar 12th, 2023. (View publication)

  13. Aggunna, M., Reddy, R., Lekkala, G.R.S. and Yedidi, R.S. (2023). An intermittent culturing protocol for Helicobacter pylori from clinical biopsies. TCABSE-J, Vol. 1, Issue 6:1-3. Oct 24th, 2023. Epub: Apr 8th, 2023. (View publication)

  14. Aggunna, M., Grandhi, A.V.K.S. and Yedidi, R.S. (2023). Molecular dynamics simulations of cytotoxin-associated gene A coded protein from Helicobacter pylori to probe the flexibility of p53 binding pocket for inhibitor design. TCABSE-J, Vol. 1, Issue 6:9-14. Oct 24th, 2023. Epub: Aug 10th, 2023. (View publication)

  15. Kizito, M.M., Dandusena, U., Aggunna, M. and Yedidi, R.S. (2024). Antimicrobial efficacy of toothpastes containing herbal vs. synthetic ingredients against antibiotic-sensitive/-resistant Gram -ve oral bacteria that cause dental caries. TCABSE-J, Vol. 1, Issue 8:9-13. Epub: July 27th, 2024. (View publication)

  16. Vissapragada, M., Addala, S., Aggunna, M., Sodasani, M., Grandhi, A.V.K.S. and Yedidi, R.S. (2024). Leveraging the potential of bacterial lateral gene transfer in boosting the efficacy of an edible probiotic prototype yogurt vaccine for COVID-19. Biochemical and Biophysical Research Communications, Vol. 734,150622. (View publication)

  17. Vissapragada, M., Aggunna, M., Tallapalli, M., Mandugula, H., Devandla, A., Yekula, A., Malapati, A., Bonala, S., Addala, S., Gudapati, S. and Yedidi, R.S. (2024) In silico prediction of COVID-19 vaccine efficacy based on the strain-specific structural deviations in the SARS CoV-2 spike protein receptor binding domain. Medical Research Archives, Vol. 12, No. 9. (View publication)

  18. Aggunna, M., Akula, N., Yanamadala, A.S., Penta, H., Geddam, S., Kota, S., Badugu, S., Muttyala, K., Sodasani, M., Kumar, R., Akondi, R.V., Panchagnula, B., Pola, S., Sala, Y., Ravuri, S., Tsalla, R. and Yedidi, R.S. (2025). Antibiotic-resistance exhibited by clinical isolates of Helicobacter pylori: reality check vs. an artifact of the in vitro assay while deciding the treatment regimen. TCABSE-J, Vol. 1, Issue 9:5-9. Epub: Nov 11 th , 2024. (View publication)

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