Computational Drug Discovery

Identification and optimization of novel therapeutic candidates through integrated in silico approaches, including virtual screening, molecular docking, molecular dynamics simulations, and structure-based drug design. Emphasis is placed on translating computational predictions into experimentally testable lead molecules with defined pharmacological potential.

Structural Biology & Molecular Mechanisms

Elucidation of protein structure, conformational dynamics, and intermolecular interactions to uncover the molecular basis of biological function and disease. By integrating structural modeling with biophysical and biochemical validation, we aim to establish mechanistic insights at atomic and near-atomic resolution.

Missense Mutation & Disease Mechanism Analysis

Comprehensive analysis of disease-associated missense variants using structural bioinformatics, stability predictions, and interaction network mapping. These studies aim to define how specific mutations perturb protein folding, dynamics, and signaling pathways, thereby contributing to pathogenesis.

Rational Design of Immunomodulators

Systematic discovery and characterization of novel immunomodulatory candidates through computational design, target identification, and experimental validation. Candidate molecules are evaluated using cell-based assays and in vivo models to establish efficacy, specificity, and mechanism of action.

Immune Reprogramming & Cytokine Profiling

Mechanistic investigation of immune modulation through cytokine profiling, immune gene expression analysis, and biochemical characterization of signaling pathways. These studies aim to define how candidate modulators reshape immune responses under inflammatory and disease conditions.

Gut Microbiota & Host–Immune Interactions

Integrated assessment of microbiome dynamics using 16S rRNA sequencing, supported by fecal metabolomics and pathway analysis. The objective is to delineate microbiota-derived metabolites and microbial shifts that influence host immune regulation and systemic health outcomes.

Ongoing

1. Project Title: Investigating Phenotypic-genotypic correlations of Ayurveda Prakriti through a multidisciplinary approach

Budget: 7,000,000 INR

Funding Agency: Ministry of Ayush (2026-2029)

Principal Investigator: Dr. Dileep K Vijayan

2. Project Title: Evaluation of the Immunomodulatory Effects of Micronized Curcumin Formulations

Budget: 1,000,000 INR

Funding Agency: Symega Food Ingredients Limited (2025-2027)

Principal Investigator: Dr. Dileep K Vijayan

3. Project Title: Toxicology studies and dosage of GI tagged sesamum oil Investigation Toxicology studies and dosage of GI tagged sesamum oil Investigation into the acute and sub-acute toxicity of sesame oil in rats

Budget: 3,000,000 INR

Funding Agency: Onattukara Vikasana Agency (2025-2026)

Principal Investigator: Dr. Dileep K Vijayan

Completed

1. Project Title: Investigation into the bioavailability and acute toxicity of micro ionized curcumin formulation in rats

Budget: 500,000 INR

Funding Agency: Symega Food Ingredients Limited (2024-2025)

Principal Investigator: Dr. Dileep K Vijayan

2. Project Title: Elucidating the role of spices as preventive and therapeutic agents for Alzheimer’s disease.

Budget: 5,008,000 INR.

Funding Agency: Spices Board, Govt. of India (2022-2025)

Principal Investigator: Dr. Dileep K Vijayan

3. Project Title: Study on the phenotypic-genotypic relations of Ayurveda prakriti through a multi-disciplinary approach

Budget: 1,500,000 INR

Funding Agency: Jubilee Mission Medical College and Research Institute.

Principal Investigator: Dr. Dileep K Vijayan

4. Project Title: Non-invasive treatment of uterine fibroids through rationally designed selective progesterone receptor modulators

Budget: 9,244,910 INR

Funding Agency: Dept. of Health Research, Govt. of India. (2021-2024)

Principal Investigator: Dr. Dileep K Vijayan

5. Project Title:  Discovery of human Glutaminyl Cyclase inhibitors for the treatment of Alzheimer's disease.

Budget: 2,400,000 JPY (approx. 1,600,000 INR).

Funding Agency: Ministry of Education Culture, Sports, Science and Technology, Govt. of Japan. (2016-2018)

Principal Investigator: Dr. Dileep K Vijayan 

Animal cell culture

In vitro analysis of cell viability, cytotoxicity and drug screening

Molecular modelling

In silico analysis of biomolecular interactions using molecular docking, molecular dynamics simulations, structure–function studies, and mutation impact assessment

Protein purification and crystallization

Isolation, purification, and crystallization of target proteins

2026

• Saritha, F., Kumar, R.A. and Dileep, K.V., 2026. Unravelling the structural impact of progesterone receptor mutations in myoma and progesterone intolerance through computational modeling. Computers in Biology and Medicine, 202, p.111476. https://doi.org/10.1016/j.compbiomed.2026.111476.
• Aiswarya, N., Remya, C., Sajitha, K., Rajan, R., Vasudevan, D.M. and Dileep, K.V., 2026. Methyl eugenol as a multitarget-directed ligand for Alzheimer disease: A promising lead for drug design. ASPET Discovery, 2.

2025

• Hima, S., Remya, C., Abhithaj, J., Arun, K. G., Sabu, A., Sajitha, K., Rajan, R., Vasudevan, D. M., &Dileep, K. V. (2025). Insights into the structural and biophysical mechanisms of benzamidine-driven inhibition of human lysozyme aggregation. International Journal of Biological Macromolecules, 141139. https://doi.org/10.1016/j.ijbiomac.2025.141139
• Babu, A., Remya, C., Sajith, A. M., Dileep, K. V., Kenchaiah, S., & Khade, A. (2025). The complex interplay between ligand strain, coulombic interactions, and binding site dynamics of two congeneric AChE inhibitors. Journal of Molecular Structure, 141479. https://doi.org/10.1016/j.molstruc.2025.141479
• Sajitha, K., Rao, K. Y., Yesu, V. B., Remya, C., Dileep, K. V., Narayana, V. V. P. C., Basha, S. J., Vamsi, K., Babu, D. S., Murali, V., Ganesh, V., Damu, A. G., Srinivasulu, D., & Vijaya, J. N. V. (2025). Design, synthesis, characterization and in vitro evaluation of anticholinesterase and antioxidant activities of thiazole-piperazine sulfonamide hybrids. Chemistry and Biodiversity. https://doi.org/10.1002/cbdv.202500567
• Kandrakonda, Y. R., Remya, C., Dileep, K. V., Shaik, J. B., Gajula, N. N., &Mothukuru, S. (2025). Quinazolinone acrylamides as anti-Alzheimer agents: Unravelling their modulating efficacy on amyloidogenic peptide assembly at molecular level. ACS Chemical Neuroscience. https://doi.org/10.1021/acschemneuro.5c00062
• Hima, S., Aiswarya, N., Remya, C., Vasudevan, D. M., Dileep, K. V., & Dileep, F. (2025). Deciphering protein aggregation: Insights into morphology, factors, and diseases. Advances in Protein Chemistry and Structural Biology. https://doi.org/10.1016/bs.apcsb.2024.11.009
• Dileep, K. V., Sakai, N., Ihara, K., Nakata, A., Ito, A., Sivaraman, D. M., & Yip, C. W. (2025). Identification of benzimidazole-6-carboxamide based inhibitors of secretory glutaminyl cyclase for the treatment of Alzheimer's disease. International Journal of Biological Macromolecules, 293, 139320. https://doi.org/10.1016/j.ijbiomac.2024.139320
• Kumar, S.S., Remya, C., Krishnakumar, K., Maria, E., Dileep, K.V. and John, M., 2025. Modulation of COX-2, 5-LOX, and cytokine signalling by Carica papaya L. Leaf cultivar Red Lady flavonoids in inflammation: in-vitro and in-silico insights. Natural Product Research, pp.1-7.
• Aiswarya, N., Hima, S., Remya, C., Vasudevan, D.M., Dileep, K.V. and Francis, D., 2025. Molecular blueprints: Guiding drug discovery through protein structure analysis. Advances in Protein Chemistry and Structural Biology, 147, pp.37-99.
• Paul, S., Chandran, R., Vijayan, D.K., Bhardwaj, J., Singh, P., Shetty, P., Cheruku, S., Meleveetil, S. and Krishnamma, B.B., 2025. A Cdk5 inhibitor restores cognitive function and alleviates type 2 diabetes in mice. iScience, 28(4).

2024

• Hima, S., Remya, C., Sadasivan, C., & Dileep, K. V. (2024). Carboxylic acid derivatives suppress the growth of Aspergillus flavus through the inhibition of fungal alpha-amylase. Journal of Biomolecular Structure and Dynamics, 42(7), 3563-3567. https://doi.org/10.1080/07391102.2023.2214464
• Yelamanda Rao, K., Chandran, R., Dileep, K. V., Gorantla, S. C., & Basha, S. J. (2024). Quinazolinone-hydrazine cyanoacetamide hybrids as potent multitarget-directed druggable therapeutics against Alzheimer's disease: Design, synthesis, and biochemical, in silico. ACS Chemical Neuroscience, 15(18), 3401-3420. https://doi.org/10.1021/acschemneuro.4c00260
• Remya, C., Aiswarya, N. and Dileep, K.V., 2024. Unveiling Nature's Arsenal: Natural Sources for Drug Discovery in Alzheimer's Disease. In Drugs from Nature: Targets, Assay Systems and Leads (pp. 333-366). Singapore: Springer Nature Singapore.

2023

• Saritha, F., Aiswarya, N., Aswath Kumar, R., & Dileep, K. V. (2023). Structural analysis and ensemble docking revealed the binding modes of selected progesterone receptor modulators. Journal of Biomolecular Structure and Dynamics, 41(21), 12401-12410. https://doi.org/10.1080/07391102.2022.2147746
• Babu, A., John, M., Liji, M. J., Maria, E., Bhaskar, S. J., Binukmar, B. K., Sajith, A. M., Reddy, E. K., Dileep, K. V., & Sunil, K. (2023). Sub-pocket-focused designing of tacrine derivatives as potential acetylcholinesterase inhibitors. Computers in Biology and Medicine, 155, 106666. https://doi.org/10.1016/j.compbiomed.2023.106666 (Babu_2023_Comput.Biol.Med_155_106666 - bioweb.supagro.inrae.fr)
• Liggri, P. G. V., Prez-Garrido, A., Tsitsanou, K. E., Dileep, K. V., Michaelakis, A., Papachristos, D. P., Prez-Snchez, H., & Zographos, S. E. (2023). 2D fingerprinting and molecular docking studies identified potent mosquito repellents targeting odorant binding protein 1. Insect Biochemistry and Molecular Biology, 157, 103961. https://doi.org/10.1016/j.ibmb.2023.103961
• Balaram, N., Jose, J., Gafoor, A., Balachandran, S., Saritha, F., Dileep, K. V., & Balan, S. (2023). Acetazolamide responsive early-onset absence epilepsy and ataxia in a toddler with a KCNA2 genetic variant: A case report. Seizure: European Journal of Epilepsy, 110, 157-159. https://doi.org/10.1016/j.seizure.2023.06.004
• Remya, C., Dileep, K. V., Variyar, E. J., Omkumar, R. V., & Sadasivan, C. (2023). Lobeline: A multifunctional alkaloid modulates cholinergic and glutamatergic activities. IUBMB Life, 75(10), 844-855. https://doi.org/10.1002/iub.2920
• Remya, C., Variyar, E. J., Omkumar, R. V., Sadasivan, C., &Dileep, K. V. (2023). Unveiling the molecular basis of lobeline's allosteric regulation of NMDAR: Insights from molecular modeling. Scientific Reports, 13(1), 22418. https://doi.org/10.1038/s41598-023-49735-4

2022

• Viswanadhapalli, S., Dileep, K. V., Zhang, K. Y. J., Nair, H. B., & Vadlamudi, R. K. (2022). Targeting LIF/LIFR signaling in cancer. Genes & Diseases, 9(4), 973-980. https://doi.org/10.1016/j.gendis.2021.04.003
• Gupta, P., Kadamberi, I. P., Mittal, S., Tsaih, S. W., George, J., Kumar, S., Vijayan, D. K., Geethadevi, A., Parashar, D., Topchyan, P., McAlarnen, L., Volkman, B. F., Cui, W., Zhang, K. Y. J., Di Vizio, D., Raghavan, P. C., & Pradeep, S. (2022). Tumor derived extracellular vesicles drive T cell exhaustion in tumor microenvironment through sphingosine mediated signaling and impacting immunotherapy outcomes in ovarian cancer. Advanced Science, 9(14), 2104452. https://doi.org/10.1002/advs.202104452
• Dileep, K. V., Ihara, K., Mishima-Tsumagari, C., Kukimoto-Niino, M., Yonemochi, M., Hanada, K., Shirouzu, M., & Zhang, K. Y. J. (2022). Crystal structure of human acetylcholinesterase in complex with tacrine: Implications for drug discovery. International Journal of Biological Macromolecules, 210, 172-181. https://doi.org/10.1016/j.ijbiomac.2022.03.097
• Aiswarya, N., Remya, C., Remashree, A. B., Sadasivan, C., & Dileep, K. V. (2022). Binding of rosmarinic acid, curcumin, and capsaicin with PLA2: A comparative study. Biochemical and Biophysical Research Communications, 626, 187-191. https://doi.org/10.1016/j.bbrc.2022.09.063

2021

• Dileep, K. V., Sakai, N., Ihara, K., Murayama, M. K., Nakata, A., Ito, A., Sivaraman, D. M., Shin, J. W., Yoshida, M., Shirouzu, M., & Zhang, K. Y. J. (2021). Piperidine-4-carboxamide as a new scaffold for designing secretory glutaminyl cyclase inhibitors. International Journal of Biological Macromolecules, 170, 415-423. https://doi.org/10.1016/j.ijbiomac.2020.12.066
• Remya, C., Dileep, K. V., Variyar, E. J., Zhang, K. Y. J., Omkumar, R. V., & Sadasivan, C. (2021). Chemical similarity-assisted search for acetylcholinesterase inhibitors: Molecular modeling and evaluation of their neuroprotective properties. International Journal of Biological Macromolecules, 174, 466-476. https://doi.org/10.1016/j.ijbiomac.2021.01.035
• Janezic, M., Dileep, K. V., & Zhang, K. Y. J. (2021). A multidimensional computational exploration of congenital myasthenic syndrome-causing mutations in human choline acetyltransferase. Journal of Cellular Biochemistry, 122(8), 787-800. https://doi.org/10.1002/jcb.29740
• Balan, S., Iwayama, Y., Ohnishi, T., Fukuda, M., Shirai, A., Yamada, A., Weirich, S. M. K., Dileep, K. V., Endo, T., & Hisano, Y. (2021). A loss-of-function variant in SUV39H2 identified in autism-spectrum disorder causes altered H3K9 trimethylation and dysregulation of protocadherin -cluster genes in the developing brain. Molecular Psychiatry, 26(12), 7550-7559. https://doi.org/10.1038/s41380-021-01183-1
• Remya, C., Dileep, K. V., Reddy, E. K., Mantosh, K., Lakshmi, K., Jacob, R. S., Sajith, A. M., Variyar, E. J., Anwar, S., Zhang, K. Y. J., & Sadasivan, C. (2021). Neuroprotective derivatives of tacrine that target NMDA receptor and acetyl cholinesterase design, synthesis and biological evaluation. Computational and Structural Biotechnology Journal, 19, 4517-4537. https://doi.org/10.1016/j.csbj.2021.08.010
• Chandran, R., & Dileep, K. V. (2021). Exploring the binding mode of PQ912 against secretory glutaminyl cyclase through systematic exploitation of conformational ensembles. Chemical Biology & Drug Design, 98(5), 850-856. https://doi.org/10.1111/cbdd.13910