M.Sc., CSIR-JRF, GATE and Ph.D. in Computational Chemistry

Quantum Chemistry, Solid State, Chemical Kinetics, Thermodynamics, Chemical & Ionic Equilibria, Coordination Chemistry, Molecular Modelling and Artificial Intelligence, Organometallic Chemistry, Application of Computer in Chemistry, S & P Block elements, d-Block elements, Thermochemistry, Chemical Bonding, Atomic Structure and Spectroscopy

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Oxazolidine based nsP3 Protease of CHIKV Inhibitor: Designing, Virtual Screening, Docking and Molecular Dynamics Simulations

SIP: In-silico Study of Pesticides for the Binding of Calyx of Bovine β-Lactoglobulin.

1. Aslam, M.; Singh, M. B.; Singh, P.; Pandey, G.; Kumar, A.; Singh, S.; Tumba, K.; Chopra, H.; Kumar, D.; Kumari, K. Impact of functional group positioning in the anion of ionic liquids on aqueous solubility: a study through DFT calculations in Ionics (Springer Berlin Heidelberg), November 28, 2023, 1-13. (Impact Factor: 2.961).
2. Raman, A. P. S.; Pongpaiboon, S.; Bhatia, R.; Dabodhia, K. L.; Kumar, A.; Kumar, D.; Jain, P.; Sagar, M.; Singh, P.; Kumari, K. In silico study on antidiabetic and antioxidant activity of bioactive compounds in Ficus carica L in Journal of Biomolecular Structure and Dynamics, August 6, 2023, 41 1-17. (Impact Factor: 5.235).
3. Kumar, D.; Kumari, K.; Chandra, R.; Jain, P.; Vodwal, L.; Gambhir, G.; Singh, P. A review targeting the infection by CHIKV using computational and experimental approaches in Journal of Biomolecular Structure and Dynamics. 2022, 1-15. (Impact Factor: 5.235)
4. Singh, M. B.; Sharma, R.; Kumar, D.; Khanna, P.; Mansi., Khanna, L.; Kumar, V.; Kumari, K.; Gupta, A.; Chaudhary, P.; Kaushik, N.; Choi, E. W.; Kaushik, N. K.; Singh, P. An understanding of coronavirus and exploring the molecular dynamics simulations to find promising candidates against the Mpro of nCoV to combat the COVID-19: A systematic review in Journal of Infection and Public Health, 2022, 15, 1326-1349. (Impact Factor: 7.7)
5. Meena, M. K.; Kumar, D.; Kumari, K.; Kaushik, N. K.; Kumar, R. V.; Bahadur, I.; Vodwal, L.; Singh, P. Promising inhibitors of nsp2 of CHIKV using molecular docking and temperature-dependent molecular dynamics simulations in Journal of Biomolecular Structure and Dynamics. 2022, 40 (13), 5827-5835. (Impact Factor: 5.235)
6. Kumar, A.; Kumar, D.; Kumar, R.; Singh, P.; Chandra, R.; Kumari, K. DFT and docking studies of designed conjugates of noscapines & repurposing drugs: promising inhibitors of main protease of SARS-CoV-2 and falcipan-2 in Journal of Biomolecular Structure and Dynamics. 2022, 40 (6), 2600-2620. (Impact Factor: 5.235)
7. Meena, M. K.; Kumar, D.; Jayaraj, A.; Kumar, A.; Kumari, K.; Katata-Seru, L.; Bahadur, I.; Kumar, V.; Sherawat, A.; Singh, P. Designed thiazolidines: An arsenal for the inhibition of nsP3 of CHIKV using molecular docking and MD simulations in Journal of Biomolecular Structure and Dynamics. 2022, 40 (4), 1607-1616. (Impact Factor: 5.235)
8. Singh, P.; Kumar, D.; Pal, S.; Kumari, K.; Bahadur, I. L-amino-acids as immunity booster against COVID-19: DFT, molecular docking and MD Simulations in Journal of molecular structure. 2022, 1250, 131924. (Impact Factor: 3.841)
9. Kumar, D.;  Meena, M. K.;  Kumar, V.;  Singh, P.; Bahadur, I., Impact of Temperature on Structural Changes in nsp2 and nsp3 of CHIKV: Molecular Dynamics Simulations in Research Square. 2022, 1-9.
10. Kumar, A.; Kumari, K.; Raman, A. P. S.; Jain, P.; Kumar, D.; Singh, P. An insight for the interaction of drugs (acyclovir/ganciclovir) with various ionic liquids: DFT calculations and molecular docking in Journal of Physical Organic Chemistry. 2022, 35 (1), e4287. (Impact Factor: 2.155)
11. Kumar, D.; Kumari, K.; Vishvakarma, V. K.; Jayaraj, A.; Kumar, D.; Ramappa, V. K.; Patel, R.; Kumar, V.; Dass, S. K.; Chandra, R. Promising inhibitors of main protease of novel corona virus to prevent the spread of COVID-19 using docking and molecular dynamics simulation in Journal of Biomolecular Structure and Dynamics. 2021, 39 (13), 4671-4685. (Impact Factor: 5.235)
12. Kumar, D.; Meena, M.; Kumari, K.; Kumar, R.; Bahadur, I.; Jain, P.; Singh, P. Exploring the effect of temperature on inhibition of non-structural protease 3 of Chikungunya virus using molecular dynamics simulations and thermodynamics parameters in Journal of Molecular Liquids. 2021, 335, 116164. (Impact Factor: 6.633)
13. Kumar, D.; Kumari, K.; Jayaraj, A.; Kumar, V.; Kumar, R. V.; Dass, S. K.; Chandra, R.; Singh, P. Understanding the binding affinity of noscapines with protease of SARS-CoV-2 for COVID-19 using MD simulations at different temperatures in Journal of Biomolecular Structure and Dynamics. 2021, 39 (7), 2659-2672. (Impact Factor: 5.235)
14. Kumar, A.; Kumar, D.; Kumari, K.; Mkhize, Z.; Katata Seru, L. M.; Bahadur, I.; Singh, P. Metal-ligand complex formation between ferrous or ferric ion with syringic acid and their anti-oxidant and anti-microbial activities: DFT and molecular docking approach in Journal of Molecular Liquids. 2021, 322, 114872. (Impact Factor: 6.633).
15. Kumari, K.; Kumar, D.; Kumar, R. V.; Singh, P. Kuwanons, promising inhibitors against the ACE-2, main protease of SARS-CoV-2 and falcipan-2 using molecular docking in Research Square. 2020, 1-15
16. Kumar, D.;  Kumari, K.;  Bahadur, I.; Singh, P., Promising Acyclovir and its derivatives to inhibit the protease of SARS-CoV-2: Molecular Docking and Molecular Dynamics simulations in  Research Square. 2020, 1-17.
17. Kumar, D.;  Kumari, K.; Singh, P., A Theoretical Model to Study the Interaction Between Boronic Acids and Insulin in ChemRxiv. 2020, 1-14.
18. Kumar, D.; Meena, M. K.; Kumari, K.; Patel, R.; Jayaraj, A.; Singh, P. In-silico prediction of novel drug-target complex of nsp3 of CHIKV through molecular dynamic simulation in Heliyon. 2020, 6 (8), e04720. (Impact Factor: 3.776)
19. Kumar, D.; Kumari, K.; Jayaraj, A.; Singh, P. Development of a theoretical model for the inhibition of nsP3 protease of Chikungunya virus using pyranooxazoles in Journal of Biomolecular Structure and Dynamics. 2020, 38 (10), 3018-3034. (Impact Factor: 5.235)
20. Kumar, D.; Singh, P.; Jayaraj, A.; Kumar, V.; Kumari, K.; Chandra, R.; Ramappa, V. K. Selective Docking of Pyranooxazoles Against nsP2 of CHIKV Eluted Through Isothermally and Non?Isothermally MD simulations in ChemistrySelect. 2020, 5 (14), 4210-4220. (Impact Factor: 2.307)
21. Azad, I.; Akhter, Y.; Khan, T.; Azad, M. I.; Chandra, S.; Singh, P.; Kumar, D.; Nasibullah, M. Synthesis, quantum chemical study, AIM simulation, in silico ADMET profile analysis, molecular docking and antioxidant activity assessment of aminofuran derivatives in Journal of Molecular Structure. 2020, 1203, 127285. (Impact Factor: 3.841)
22. Singh, P.;  Kumar, D.;  Vishvakarma, V. K.;  Yadav, P.;  Jayaraj, A.; Kumari, K. Computational approach to study the synthesis of noscapine and potential of stereoisomers against nsP3 protease of CHIKV in Heliyon. 2019, 5 (12). (Impact Factor: 3.776).
23. Kumar, D.; Singh, P.; Jayaraj, A.; Kumar, V.; Kumari, K.; Patel, R. A theoretical model to study the interaction of erythro?noscapines with nsP3 protease of Chikungunya virus in ChemistrySelect. 2019, 4 (17), 4892-4900. (Impact Factor: 2.307).
24. Singh, P.; Kumari. K.; Vishvakarma, V. K.; Mehrotra, G. K.; Chandra, R.; Kumar, D.; Patel, R.; Shahare, V. V. Metal NPs (Au, Ag and Cu): Synthesis, Stabilization and their Role in green chemistry and drug Delivery in Springer International Publishing AG. 2017, 1, 309-337. (Impact Factor: 3.182).
25. Kumar, D.; Kumari, K.; Vishvakarma, V. K.; Singh, P.; Chandra, R.; Athar, M. Sulphonylurea, Metformin, TZDs: Potential drugs to cure Diabetes in International J. Advanced Biomed. 2017, 1, 11-18. (Impact Factor: 0.034).
26. Kumar, D.; Singh, P.; Chandra, R.; Kumari, K.; Kumar, M. Impact of Gemini Surfactants on the stability of Insulin using computational tools in J Nanomed Biother. 2017, 7, 1-5. (Impact Factor: 3.687)
27. Kumar, D.; Athar, M.; Kumar, G. Methods And Techniques Employed For Sugar Decolorization in LAP LAMBERT Academic Publishing. 2014, 1, 1-72.

1. Poster presentation in “National Seminar on Biophysika” at centre for interdisciplinary research in basic science Jamia Millia Islamia, New Delhi 110025 on 20 November 2018.
2. Poster presentation in “Recent Frontiers in Chemistry” in Department of Chemistry, HNB Garhwal University, Srinagar Garhwal – 246174 Uttarakand from 27th-28th April,2018.
3. Poster presentation in “National Science Day 2018” jointly organized by Indian Academy of Science, Bangalore and Indian National Science Academy, Delhi on 28 February 2018 at INSA Delhi, India.
4. Poster presentation in “Recent Advance in Chemical Sciences towards Green & Sustainable Environment: Swachh Bharat Abhiyan Perspective” at Aditi Mahavidyalaya (University of Delhi) New Delhi on 10-11 Oct. 2017.
5. Poster presentation in “National Seminar on Biophysics” at centre for interdisciplinary research in basic science Jamia Millia Islamia, New Delhi 110025 on2017.
6. Presented poster in “Trendsin Research and Innovations in Life Sciences” at Undergraduate level” in DDU College University of Delhi on 30 March 2016.

1. Oral presentation in “sustainable Future for Humanity: The new learning curve” at Maitreyi College, University of Delhi, New Delhi, India on 24 February, 2021.
2.  Participated in one week national online FDP jointly organized by Guru Angad Dev Teaching Learning Centre, SGTB Khalsa College, University of Delhi, New Delhi, India from 15 December, 2021 to 21 December, 2021. 
3. Participated in “Bioinformatics Workshop on Genomics, Proteomics, Drug Design and High Performance Computing” at the Supercomputing Facility for Bioinformatics and Computing Biology, Indian Institute of Technology Delhi from 8th-14th December 2018.
4. Participated in “One day workshop on Molecular Modelling” at Atma Ram Sanatan Dharma College, University of Delhi, New Delhi on 3rd January 2018.
5. Participated in “One day workshop on Archival Sciences” at Atma Ram Sanatan Dharma College, University of Delhi, New Delhi on 20 February 2018.
6. Participated in “One day Faculty Development Programme” at Atma Ram Sanatan Dharma College, University of Delhi, New Delhi on 10th November 2017.

Hands on Computational tools to develop biologically potential candidates:-

ChemDraw and Marvin Sketch

It is the drawing tool of choice for chemists to create or design compound library.

iGEMDOCK

It is an integrated and easy to use environment which is especially useful for post-screening analysis and inferring pharmacological interactions from screening compounds.

RASPD

A web server for preliminary screening of drug molecules from ZINC database and screening from designed compound libraries on the basis of binding affinity (ΔG).

Gaussian 09

It is used for geometry optimization, transition state, intermediate, HOMO-LUMO gap and reaction mechanism study through DFT theory.

Notepade++;

It was used for the preparation of target protein and adding of some missing atoms/ions and removal of some extra atoms/ions.

AADS

Active site or drug site on target protein was predicated by AADS web server.

ParDOCK

It is used for selective or rigid docking of drug molecules into the cavity of target protein.

Pymol; MMV; Chemira; LigPlus; Discovery Studio.

These are computer based software, a molecular visualization system and it can produce high-quality 3D images of small molecules, biological macromolecules, such as proteins and drug-target complex systems.

Gusar; Swiss ADME; Molinspiration

A web server for prediction of Acute toxicity and biological activity score of top screened molecules.

AMBER18

Amber is a suite of bio-molecular simulation programs and it was used to simulate drug-target complex and also predicted binding affinity of drug-target complex through MM-GBSA method.