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  • TRANSLATIONAL HEALTH SCIENCE AND TECHNOLOGY INSTITUTE
    AN INSTITUTE OF BIOTECHNOLOGY RESEARCH AND INNOVATION COUNCIL
    DEPT. OF BIOTECHNOLOGY, MINISTRY OF SCIENCE AND TECHNOLOGY
    GOVT OF INDIA
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DR.ASHISH KUMAR AGRAHARI

PhD (integrated) in Computational Biology, Thesis entitled “Integrating Computational Methods to Predict the Impact of Missense Mutations in Charcot Marie Tooth Disease”, Vellore Institute of tech

MKB-YRFP FELLOW

  • PhD (integrated) in Computational Biology Vellore Institute of technology University, Vellore, Tamil Nadu
  • B.Tech in Bioinformatics, Vellore Institute of technology University, Vellore, Tamil Nadu

Research Experience

M K BHAN – Young Researcher Fellow (Oct-2021 - Continue)

Non Communicable Disease (NCD), THSTI

Senior Research Associate (Aug 2020 - Sep 2021)

Non Communicable Disease (NCD), THSTI

Postdoc Researcher (Jul 2019 - Dec 2019)

Shenzhen Institutes of Advanced Technology - Chinese Academy of Sciences (SIAT - CAS), Shenzhen, China

 

Bio-Sketch

He received B.Tech in bioinformatics (2014) and PhD in computational biophysics (2018) from Vellore Institute of Technology, India. During his PhD, he focused on computational studies (in silico SNP prediction, computer-based models, molecular docking, and molecular dynamics simulations of cytoplasmic and membrane proteins), which led to the advancement of new treatments for Charcot Marie Tooth disease. During his first postdoctoral experience (2019) from Shenzhen Institutes of Advanced Technology - Chinese Academy of Science (SIAT-CAS), China, he investigated the molecular and structural aspect of GPCR. In 2020, he received MK Bhan fellowship with the host institution THSTI, where he is currently working to shed light on the molecular process and changed conformational state of protein associated with NASH disease. His broad goal is to comprehend the atomistic level details interactions of protein and its partner (ligand, peptide, protein and nucleic acids) using techniques of computational biophysics and structural bioinformatics that help to drive and improvise the development of targeted therapeutics for NASH.

 

Research interest

Computational Biophysics, Structural Bioinformatics, Computational Biology, Computer Aided Drug Discovery, Biological Modeling, Biomolecular simulation.

 

Area of Interest

Proteins seldom behave as separate entities in the majority of cases. Protein–protein interactions (PPIs) are required for appropriate biological processes. An altered PPIs led to the disease condition. As a result, my research interest is to explore the molecular basis of the disease and to unveil the molecular mechanism and altered conformational state of protein and its interaction network associated with different types of disease using computational biophysics and structural bioinformatics approaches. The ultimate objective is to use computational models and tools to understand the atomistic level features of protein and its partner (ligand, peptide, protein, or nucleic acids) interactions in order to drive and improve the development of targeted treatments and disease prevention.

 

Publication
  1. Ashish Kumar Agrahari, Mitul Srivastava, Mrityunjay Singh, Shailendra Asthana*, ‘SARS-CoV-2 envelope protein attain Kac mediated dynamical interaction network to adopt "histone mimic" at BRD4 interface’, Journal of Biomolecular Structure and Dynamics,  5.235, 2023 Mar 12;1-15.
  2. Masthan Thamim, Ashish Kumar Agrahari, Pawan Gupta, Krishnan Thirumoorthy, ‘Rational Computational Approaches in Drug Discovery: Potential Inhibitors for Allosteric Regulation of Mutant Isocitrate Dehydrogenase-1 Enzyme in Cancers’ Molecules, 2023, 28(5), 2315.
  3. ShivKumar,RohitVerma, SandhiniSaha, AshishKumar Agrahari, ShivangiShukla, Anurag, TusharMaiti, Shailendra Asthana, C.T.Ranjith-Kumar,MilanSurjit. ‘RNA-protein interactome at the Hepatitis E virus internal ribosome entry site’, Microbiology Spectrum, (accepted
  4. Padam Singh, Srishti Rawat, Ashish Kumar Agrahari, Manisha Singh, Saurabh Chugh, Sudagar Gurcha, Albel Singh, Katherine Abrahams, Gurdyl Besra, Shailendra Asthana, Diwan Rawat, and Ramandeep Singh. “NSC19723, a thiacetazone like benzaldehyde thiosemicarbazone improves the efficacy of TB drugs in vitro and in vivo”, Microbiology Spectrum, 2022 Dec 21;10(6):e0259222.
  5. Ashish Kumar Agrahari, Madhu Dikshit, Shailendra Asthana*, ‘Crystallographic mining of ASK1 regulators to unravel the intricate PPI interfaces for the discovery of small molecule’ Computational and Structural Biotechnology Journal, Volume 20, 2022, Pages 3734-3754.
  6. Mitul Srivastava; Lovika Mittal; Anita Kumari; Ashish Kumar Agrahari; Mrityunjay Singh; Rajani Mathur; Shailendra Asthana*. “ Characterizing (un)binding mechanism of USP7 inhibitors to unravel the cause of enhanced binding potencies at allosteric checkpoint”, Protein Science, Volume31, Issue9, e4398.
  7. Ritika Khatri; Hilal Ahmad Parraya; Ashish Kumar Agrahari; Zaigham Abbas Rizvi; Rachel Kaul; Sneha Raj; Shailendra Asthana; Shailendra Mani; Sweety Samal; Amit Awasthi; Shubbir Ahmed. “Designing and characterization of a SARS-CoV-2 immunogen with receptor binding motif grafted on a protein scaffold: An epitope-focused vaccine approach”, International Journal of Biological Macromolecules, Volume 209, Part A, 1 June 2022, Pages 1359-1367
  8. Ashish Kumar Agrahari*, Enrico Pieroni, Gianluca Gatto, Amit Kumar. ‘The impact of missense mutation in PIGA associated to paroxysmal nocturnal hemoglobinuria and multiple congenital anomalies-hypotonia-seizures syndrome 2: A computational study’, Heliyon, 2019, 5(10), e02709. (*=corresponding)
  9. Ashish Kumar Agrahari, M Krishna Priya, Medapalli Praveen Kumar, Chiranjib Chakraborty, George Priya Doss. C, Siva R Hatem Zayed. ‘Understanding the structure-function relationship of HPRT1 missense mutations in association with Lesch–Nyhan disease and HPRT1-related gout by in silico mutational analysis’, Computers in biology and medicine, 2019, 107, 161-171.
  10. Ashish Kumar Agrahari, George Priya Doss C, Siva R, Hatem Zayed., ‘Molecular insights of G2019S substitution in LRRK2 kinase domain associated with Parkinson's disease: A molecular dynamics simulation approach’, Journal of Theoretical Biology, 2019, 469,163-171.
  11. Ashish Kumar Agrahari, Meghana Muskan, George Priya Doss. C, Siva R, Hatem Zayed., ‘Computational insight of K1444N substitution in NF1 gene associated with neurofibromatosis type 1 disease: A molecular modelling and dynamics approach’, Metabolic Brain Disease, 2018, 33(5), 1443-1457.
  12. Ashish Kumar Agrahari, Amit Kumar, Siva R, Hatem Zayed, George Priya Doss C., ‘Substitution impact of highly conserved arginine residue at position 75 in GJB1 gene in association with X-linked Charcot-Marie-Tooth disease: A computational study’, Journal of Theoretical Biology,2018,437, 305-317.
  13. Ashish Kumar Agrahari, George Priya Doss C. (2017), ‘A computational approach to identify a potential alternative drug with its positive impact towards PMP22’, Journal of Cellular Biochemistry, 2017, 118(11), 3730-3743.
  14. Ashish Kumar Agrahari, Sneha P., George Priya Doss C, Siva R, Hatem Zayed., ‘A profound computational study to prioritize the disease-causing mutations in PRPS1 gene’, Metabolic Brain Disease,2017, 33(2), 589-600.
  15. Ashish Kumar Agrahari, C. George Priya Doss, ‘Impact of I30T and I30M substitution in MPZ gene associated with Dejerine-Sottas syndrome type B (DSSB): A molecular modeling and dynamics’, Journal of Theoretical Biology,2015, 382, 23-33.
  16. C. George Priya Doss, B. Rajith, R. Magesh, A. Ashish Kumar. ‘Influence of the SNPs on the structural stability of CBS protein: Insight from molecular dynamics simulations’, Frontiers in Biology, 9(6), 504-518.

MK Bhan-YRFP project (Ongoing)

Title - Exploring selective ASK-1 interactome for the discovery of small molecule against NASH: a PPI driven advanced computational approach

Project on COVID-19 (THSTI)

Following the outbreak of the COVID-19 pandemic, worked on a project that showed how envelope (E) protein of SARS-CoV-2 hijacks the host BRD4 protein as well as examined its molecular understanding, which might aid in the development of treatment options against SARS-CoV-2.

Second prize in “The Bioinformatics Education Grand Challenge Eduthon” at 1st Colloquium on Bioinformatics Learning, Education and Training (CoBLET 2022) in conjunction with 11th GOBLET AGM 2022, held on 11-14th October 2022. The award was given for providing a solution in the form of cloud-based platform “A global meta-registry of bioinformatics alliance” for a cutting-edge challenge “ways of solving geographical lack of advanced training in some bioinformatics areas” with the goal to mitigate the imbalance in bioinformatics expertise and disseminate the opportunities. The prize includes two years of individual GOBLET membership and a cash reward.

MK Bhan – Young Researcher Fellowship Programme (MKB-YRFP) award(2021 session) from Department of Biotechnology (DBT), Ministry of Science and Technology, Govt. of India.

SERB-DST and Immunology Foundation travel award to attend thethe Biophysics at the Dawn of Exascale, Computers thematic meeting held at Center for Free-Electron Laser Science, in Hamburg, Germany on 16 to 20 May 2022.

 

Received best poster award in Poster presentation competition - Foundation Day 15th July 2022 at THSTI, Faridabad. Poster Title: Non-conventional PPI route to modulate the interactors of ASK1 for the discovery of small molecules against NASH.

ICGEB travel award to attend the ICGEB Sponsored Meeting "3rd Protein Biophysics at the End of the World '', held at Pontificia Universidad Catolica de Chile (UC) in Santiago, Chile on  24th to 27th  April 2018.

eChemInfo Milano workshop Gold bursary awardand Immunology Foundation travel award to attend the eChemInfo Milano workshop, which was held at the University of Milan on July 16-20, 2018.

Asia Pacific BioInformatics Network (APBioNET) travel award to attend the “International Conference on Bioinformatics (Incob 2018)”, held at Jawaharlal Nehru University (JNU), New Delhi, on 26-28 September 2018.

Selected for SERB-DST travel award to attend the "Human and Mammalian Genetics and Genomics: The 59th McKusick Short Course, at The Jackson Laboratory USA (18-27 July, 2018)".

Internship at CSIR-IGIB funded by the National Network for Mathematical and Computational Biology (NNMCB) from 13 June to 13 September 2016 under the mentorship of Dr. Mitali Mukherji.

Professional Services:

Review Editor in the Editorial Board of Precision Medicine (specialty section of Frontiers in Medicine)

Reviewer of many reputed journals such as Computers in Biology and Medicine, Heliyon, the Journal of Theoretical Biology, Journal of Biomolecular Structure and Dynamics and BBA - Molecular Basis of Disease.

Debapriyo Sarmadhikari --> Project Associate-I

Tulika Sinha --> Project Associate-I

Abhishek Choudhary --> Dissertation Internship

Joys Rachel Immanuel --> Dissertation Internship

 

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