Rational Design of Antiviral Therapeutics Sneha Dokhale, Samiksha Garse, Shine Devarajan, Vaishnavi Thakur, Shaunak Kolhapure Computational Methods for Rational Drug Design, 2025 The genetic drift of viruses modulates the random mutagenesis creating an impact on the pathogenesis of the viruses. Factors such as the ability to adapt in any host cell, mimic the host genome, and exploit the metabolic and signaling pathways to further evade the immune system are challenges that need continuous and aggressive research. Moreover, drug resistance is another inevitable concern that remains a constant parameter for any antiviral therapeutics and treatment regimes. However, the integration of Omics and increased computational power has revolutionalized and achieved a 360-degree paradigm shift in designing antiviral therapeutics, especially postpandemic. The conventional therapeutics designing methods have been entirely replaced by the rational design, wherein coherent decision-making transpires the prospective therapeutic candidates based on prior knowledge of their biological mechanisms. The chapter outlines the various approaches that can be categorized as rationalized computational designs highlighting current trends for antiviral therapies. These methods empower researchers to screen thousands of compounds to characterize and create drug indicators that can morphologically alter the viral structure leading to complete viral eradication or strengthening the hosts’ immune system.
Nanodelivery of food polyphenols for nutraceutical applications Aamena Yusuf, Tanisha Ambawat, Sneha Dokhale, Shine Devarajan, Samiksha Garse, and Polyphenols Food Nutraceutical and Nanotherapeutic Applications, 2024 Food polyphenols have gained attention because of their numerous health benefits, i.e., antidiabetic, anti-inflammatory, and immunomodulatory actions, and their key role in preventing high cholesterol, high blood sugar levels, and cancer. Food polyphenols are usually found in fruits, vegetables, and red wines. However, their use is limited in the nutraceutical industry because of their low bioavailability and bioaccessibility. Advancement in nanotechnology has unleashed the potential of green-based nanocarriers that are excellent vehicles for encasing, protecting, and delivering dietary polyphenols to the target organs. They improve the biological half-life and are adept at site-specific delivery. This chapter aims to highlight the potential of nanotechnology in the nanodelivery of food polyphenols in the nutraceutical industry. Furthermore, the potential nanocarriers and various nanodelivery systems have also been discussed, giving an overview of the process. Finally, we highlight the recent advancements in polyphenol research and nanotechnology developments. We conclude the chapter by elucidating a few challenges and prospects for the application of nanodelivery in the nutraceutical industry.
Polyphenols in food products and nutraceuticals: Bioavailability and pharmacokinetic issues Priaunsh Dutt, Yashika Shadija, Sneha Dokhale, Sweta Das, Shine Devarajan, Samiksha Garse Polyphenols Food Nutraceutical and Nanotherapeutic Applications, 2024 Polyphenols have recently been sought by scientists for their antioxidant properties and effects on human health. These compounds have been known to show some anticancer properties, reduce the risk of stroke, reduce diabetes, as well as help improve blood pressure-related issues in humans. In addition, these compounds may be used in combination with drugs. Polyphenols, however, are not efficiently absorbed by the human body because of their chemical nature, which causes them to have low bioavailability. Studies carried out on the pharmacokinetic properties of polyphenols have played a major role in revealing the pathways through which these compounds are made bioavailable. This chapter discusses the broad classification of polyphenols, their ADMET properties, bioavailability data, and recent strategies to increase the bioavailability.
Unlocking the future of healthcare: Biomarkers and personalized medicine Samiksha Garse, Divya Dalal, Sneha Dokhale, Shine Devarajan Applying Machine Learning Techniques to Bioinformatics Few Shot and Zero Shot Methods, 2024 Modernization and advancement in technology have developed a new field called Health Informatics. It is an interdisciplinary that accommodates bioinformatics, artificial intelligence (AI), and machine learning (ML) applications. Additionally, a large amount of data that travels around the global network of cloud computing has coined the term internet of things (IoT), which has fostered a new wave of innovation in the healthcare sector. This chapter provides insights into how recognition systems, self-monitoring systems, big data analysis and interpretation, etc. use AI and IoT-based models to accelerate the capabilities of providing advanced healthcare outcomes. It not only unlocks futuristic smart healthcare, but also platforms a revolutionary milestone in the medical world. Moreover, the chapter addresses the challenges of security, scalability, cost-effectiveness, standardization, and quality care encountered by the healthcare sector.
Personalized vaccinology Samiksha Garse, Sneha Dokhale, Gurnain Kaur Bhandari, Vishwa Kapadiya, Kavya Prabhakar, Shine Devarajan Developments in Applied Microbiology and Biotechnology Metabolomics for Personalized Vaccinology, 2024
Isolation and characterization of a rare polar carotenoid 1’-OH-4-keto-ϒ-carotene from an indigenously isolated Rhodococcus kroppenstedtii MH715196 Simran R Lilwani, Sneha M Dokhale, Parvathi JR, Madhavi R Vernekar Food Science and Applied Biotechnology, 2022 The catabolic diversity and biocatalytic potential in members of genus Rhodococcus makes it an ideal industrial workhouse for metabolite production. Despite their applicability, Rhodococci are least explored for carotenoids, located in their cell membrane. The goal of the present study was to identify the carotenoids of Rhodococcus kroppenstedtii MH715196. UV-Vis spectral data and molecular mass estimates showed that the principal carotenoid extracted from R. kroppenstedtii MH715196 was 1’-OH-4-keto-ϒ-carotene. Biosynthetic route of 1’-OH-4-keto-ϒ-carotene in R. kroppenstedtii MH715196 was postulated on the basis of molecular mass estimates in co-relation with putative carotenoid biosynthetic genes identified in the genome of the reference strains of R. kroppenstedtii. Three key enzymes, were then considered for phylogenetic analysis to establish the phylogenetic relationship across the Rhodococcus genus leading the way for carotenoid identification in other Rhodococcus species. The present study would be the first report on identification of a rare polar carotenoid from R. kroppenstedtii MH715196 which could be potentially explored as a food colorant in hydrophilic food matrices like jams, jellies, beverages etc.
In Silico Insights into HIV-1 Vpu-Tetherin Interactions and Its Mutational Counterparts Patil Sneha, Urmi Shah, Seetharaman Balaji Medical Sciences Basel Switzerland, 2019 Tetherin, an interferon-induced host protein encoded by the bone marrow stromal antigen 2 (BST2/CD317/HM1.24) gene, is involved in obstructing the release of many retroviruses and other enveloped viruses by cross-linking the budding virus particles to the cell surface. This activity is antagonized in the case of human immunodeficiency virus (HIV)-1 wherein its accessory protein Viral Protein U (Vpu) interacts with tetherin, causing its downregulation from the cell surface. Vpu and tetherin connect through their transmembrane (TM) domains, culminating into events leading to tetherin degradation by recruitment of β-TrCP2. However, mutations in the TM domains of both proteins are reported to act as a resistance mechanism to Vpu countermeasure impacting tetherin’s sensitivity towards Vpu but retaining its antiviral activity. Our study illustrates the binding aspects of blood-derived, brain-derived, and consensus HIV-1 Vpu with tetherin through protein–protein docking. The analysis of the bound complexes confirms the blood-derived Vpu–tetherin complex to have the best binding affinity as compared to other two. The mutations in tetherin and Vpu are devised computationally and are subjected to protein–protein interactions. The complexes are tested for their binding affinities, residue connections, hydrophobic forces, and, finally, the effect of mutation on their interactions. The single point mutations in tetherin at positions L23Y, L24T, and P40T, and triple mutations at {L22S, F44Y, L37I} and {L23T, L37T, T45I}, while single point mutations in Vpu at positions A19H and W23Y and triplet of mutations at {V10K, A11L, A19T}, {V14T, I18T, I26S}, and {A11T, V14L, A15T} have revealed no polar contacts with minimal hydrophobic interactions between Vpu and tetherin, resulting in reduced binding affinity. Additionally, we have explored the aggregation potential of tetherin and its association with the brain-derived Vpu protein. This work is a possible step toward an understanding of Vpu–tetherin interactions.
VALORIZATION OF SUN MELON PEEL WASTE: PURIFICATION AND CHARACTERIZATION OF PEROXIDASE MP Abhishek Shinde, Sneha Dokhale International Journal of Innovative Research and Review ISSN: 2347 – 4424 14 … , 2026 2026
Molecular Dynamics and Virtual Screening of Withania somnifera Phytochemicals as Potential Inhibitors of the Human NLRP9 Pyrin Domain SD Aafreen Sayed, Tushar Bodke World Journal of Advanced Engineering Technology and Sciences 18 (03), 224-240 , 2026 2026
In silico Design of sgRNA for CRISPR/Cas9-Mediated MLO Gene Mutagenesis to Reduce Powdery Mildew Susceptibility in Vitis vinifera SD Aafreen Sayed, Vaibhav Shivade, Annika Gupta, Mugdha Pathak International Journal for Research in Applied Science & Engineering … , 2026 2026
Green Tea–Mediated Fabrication of Crystalline Silver and Gold Nanoparticles with Antibacterial Properties PJ Annika Durve Gupta, Shivani Kakkar Khanna, Pooja Gupta, Minal Trivedi ... Journal of Xidian University 20 (3), 243-250 , 2026 2026
Rational Design of Antiviral Therapeutics S Dokhale, S Garse, S Devarajan, V Thakur, S Kolhapure Computational Methods for Rational Drug Design, 423-443 , 2025 2025 Citations: 4
Personalized vaccinology S Garse, S Dokhale, GK Bhandari, V Kapadiya, K Prabhakar, S Devarajan Metabolomics for Personalized Vaccinology, 1-33 , 2024 2024 Citations: 1
PERSONALISED MEDICINE AS THE PROMISING IMPLICATION FOR HEALTHCARE SG Sneha Dokhale Mugdha Dabir Pathak, Kirti Futuristic Trends in Biotechnology 3 , 2024 2024
Unlocking the Future of Healthcare: Biomarkers and Personalized Medicine S Garse, D Dalal, S Dokhale, S Devarajan Applying Machine Learning Techniques to Bioinformatics: Few-Shot and Zero … , 2024 2024
Polyphenols in food products and nutraceuticals: bioavailability and pharmacokinetic issues P Dutt, Y Shadija, S Dokhale, S Das, S Devarajan, S Garse Polyphenols: Food, Nutraceutical, and Nanotherapeutic Applications, 343-360 , 2023 2023 Citations: 2
Nanodelivery of Food Polyphenols for Nutraceutical Applications A Yusuf, T Ambawat, S Dokhale, S Devarajan, S Garse Polyphenols: Food, Nutraceutical, and Nanotherapeutic Applications, 312-342 , 2023 2023 Citations: 1
Ocean Monitoring to save Marine Ecosystem S Dokhale, M Pathak Literature, Environment & Sustainibility 1 , 2023 2023
Isolation and characterization of a rare polar carotenoid 1’-OH-4-keto-ϒ-carotene from an indigenously isolated Rhodococcus kroppenstedtii MH715196 MRV Simran R. Lilwani , Sneha M. Dokhale , Parvathi J. R Food Science and Applied Biotechnology, 199-210 , 2022 2022 Citations: 1
In Silico Insights into HIV-1 Vpu-Tetherin Interactions and Its Mutational Counterparts S Patil, S Urmi, B Seetharaman Medical Sciences 7 (6) , 2019 2019 Citations: 3
Structural discordance in HIV-1 Vpu from brain isolate alarms amyloid fibril forming behavior-a computational perspective P Sneha, PK Panda, FR Gharemirshamlu, K Bamdad, S Balaji Journal of Theoretical Biology 451, 35-45 , 2018 2018 Citations: 4
Combined gene expression analysis in HIV Associated Dementia, Alzheimer’s disease and Parkinson’s disease-an in-silico approach NP Sneha Dokhale, Yash Shah IJCB 7 (1), 52-59 , 2018 2018 Citations: 3
Amyloidogenic pattern prediction of HIV-1 proteins P Sneha, B Seetharaman, P Shapshak Global Virology II-HIV and NeuroAIDS, 823-895 , 2017 2017 Citations: 1
IDENTIFICATION OF METALLOPROTEASES LIKE DOMAIN IN TRITICUM AESTIVUM α/β GLIADIN PROTEIN FROM BIOINFORMATICS PERSPECTIVE: A HYPOTHESIS C Selvaa Kumar, S Dokhale 2017
AFPep as Curative Mediator of Breast Cancer: An Insilico Approach P Priyam, P Pritam, P Sneha LAP LAMBERT Academic Publishing , 2016 2016
Global Protein Sequence Variation in HIV-1-B Isolates Derived from Human Blood and Brain SP Balaji Seetharaman, Sneha Patil, Rama Murugappan Global Virology I - Identifying and Investigating Viral Diseases , 2015 2015 Citations: 7
In-silico stability analysis and phosphorylation induced structural simulation of alpha-synuclein in Parkinson's disease PK Panda, S Patil, P Patel Research and Reviews. J. Bioinforma 2 (1), 15-21 , 2015 2015 Citations: 3
MOST CITED SCHOLAR PUBLICATIONS
Global Protein Sequence Variation in HIV-1-B Isolates Derived from Human Blood and Brain SP Balaji Seetharaman, Sneha Patil, Rama Murugappan Global Virology I - Identifying and Investigating Viral Diseases , 2015 2015 Citations: 7
Rational Design of Antiviral Therapeutics S Dokhale, S Garse, S Devarajan, V Thakur, S Kolhapure Computational Methods for Rational Drug Design, 423-443 , 2025 2025 Citations: 4
Structural discordance in HIV-1 Vpu from brain isolate alarms amyloid fibril forming behavior-a computational perspective P Sneha, PK Panda, FR Gharemirshamlu, K Bamdad, S Balaji Journal of Theoretical Biology 451, 35-45 , 2018 2018 Citations: 4
Mutation based structural modelling and dynamics study of alpha fetoprotein: an insight to inhibitory mechanism in breast cancer H Panchal Journal of Proteomics & Bioinformatics , 2008 2008 Citations: 4
In Silico Insights into HIV-1 Vpu-Tetherin Interactions and Its Mutational Counterparts S Patil, S Urmi, B Seetharaman Medical Sciences 7 (6) , 2019 2019 Citations: 3
Combined gene expression analysis in HIV Associated Dementia, Alzheimer’s disease and Parkinson’s disease-an in-silico approach NP Sneha Dokhale, Yash Shah IJCB 7 (1), 52-59 , 2018 2018 Citations: 3
In-silico stability analysis and phosphorylation induced structural simulation of alpha-synuclein in Parkinson's disease PK Panda, S Patil, P Patel Research and Reviews. J. Bioinforma 2 (1), 15-21 , 2015 2015 Citations: 3
Polyphenols in food products and nutraceuticals: bioavailability and pharmacokinetic issues P Dutt, Y Shadija, S Dokhale, S Das, S Devarajan, S Garse Polyphenols: Food, Nutraceutical, and Nanotherapeutic Applications, 343-360 , 2023 2023 Citations: 2
Personalized vaccinology S Garse, S Dokhale, GK Bhandari, V Kapadiya, K Prabhakar, S Devarajan Metabolomics for Personalized Vaccinology, 1-33 , 2024 2024 Citations: 1
Nanodelivery of Food Polyphenols for Nutraceutical Applications A Yusuf, T Ambawat, S Dokhale, S Devarajan, S Garse Polyphenols: Food, Nutraceutical, and Nanotherapeutic Applications, 312-342 , 2023 2023 Citations: 1
Isolation and characterization of a rare polar carotenoid 1’-OH-4-keto-ϒ-carotene from an indigenously isolated Rhodococcus kroppenstedtii MH715196 MRV Simran R. Lilwani , Sneha M. Dokhale , Parvathi J. R Food Science and Applied Biotechnology, 199-210 , 2022 2022 Citations: 1
Amyloidogenic pattern prediction of HIV-1 proteins P Sneha, B Seetharaman, P Shapshak Global Virology II-HIV and NeuroAIDS, 823-895 , 2017 2017 Citations: 1
VALORIZATION OF SUN MELON PEEL WASTE: PURIFICATION AND CHARACTERIZATION OF PEROXIDASE MP Abhishek Shinde, Sneha Dokhale International Journal of Innovative Research and Review ISSN: 2347 – 4424 14 … , 2026 2026
Molecular Dynamics and Virtual Screening of Withania somnifera Phytochemicals as Potential Inhibitors of the Human NLRP9 Pyrin Domain SD Aafreen Sayed, Tushar Bodke World Journal of Advanced Engineering Technology and Sciences 18 (03), 224-240 , 2026 2026
In silico Design of sgRNA for CRISPR/Cas9-Mediated MLO Gene Mutagenesis to Reduce Powdery Mildew Susceptibility in Vitis vinifera SD Aafreen Sayed, Vaibhav Shivade, Annika Gupta, Mugdha Pathak International Journal for Research in Applied Science & Engineering … , 2026 2026
Green Tea–Mediated Fabrication of Crystalline Silver and Gold Nanoparticles with Antibacterial Properties PJ Annika Durve Gupta, Shivani Kakkar Khanna, Pooja Gupta, Minal Trivedi ... Journal of Xidian University 20 (3), 243-250 , 2026 2026
PERSONALISED MEDICINE AS THE PROMISING IMPLICATION FOR HEALTHCARE SG Sneha Dokhale Mugdha Dabir Pathak, Kirti Futuristic Trends in Biotechnology 3 , 2024 2024
Unlocking the Future of Healthcare: Biomarkers and Personalized Medicine S Garse, D Dalal, S Dokhale, S Devarajan Applying Machine Learning Techniques to Bioinformatics: Few-Shot and Zero … , 2024 2024
Ocean Monitoring to save Marine Ecosystem S Dokhale, M Pathak Literature, Environment & Sustainibility 1 , 2023 2023
IDENTIFICATION OF METALLOPROTEASES LIKE DOMAIN IN TRITICUM AESTIVUM α/β GLIADIN PROTEIN FROM BIOINFORMATICS PERSPECTIVE: A HYPOTHESIS C Selvaa Kumar, S Dokhale 2017
