Manvi
Scientist
Bengaluru
Overview
14
14
years of professional experience
Work History
Scientist
Aurigene Pharmaceutical Services Limited, APSL
03.2022 - Current
- Supporting various projects aiming to identify novel small molecules targeting different protein targets.
- Supported internal project with POC study where I contributed towards project planning, design prioritization and compound selection. Team successfully identified 6 active compounds, where 2 compounds were novel.
- PROTAC platform: Helping in setting up the PROTAC pipeline which includes ternary complex prediction, PROTAC degradation prediction and PROTAC design. Supported ideating and prioritizing selected PROTACs designs for synthesis and testing which resulted in notable success.
- Supported reaction-based compound library enumeration.
- Supported in generating various high quality project proposals. Few of the projects are onboarded.
- Lead one project where I proposed new core along with various other designs. Few of the compounds generated with this core showed one digit micromolar activity.
Project Scientist I
CCBT, InStem, NCBS
09.2018 - 03.2022
- Supported various projects to create small molecule probe that modulate novel classes of targets.
- Supported design of partner peptide constructs based on experimental data along with the help of In-silico tools. For one of the projects, out of three peptide constructs one showed affinity in single digit micromolar and another in two-digit micromolar.
- Predicted putative binding poses for partner peptides in couple of projects.
- Predicted possible binding poses for small molecules targeting PPIs based on experimental data and was able to explain the SAR. Also working on the binding pose prediction for experimentally obtained fragment hits for one of the PPI target.
- Done MD simulation to support the observation of experimental crystal structure data. Work is published.
- Used Ligand- and Structure-based Virtual Screening followed by MD simulation for one of the microbial targets to identify novel inhibitors. Work is published.
- For one of the client projects, predicted small molecules binding poses and suggested pocket mutations to validate the pose. Experimental evidence was pending.
- Provided inputs for various targets ideation.
Sr. Research Associate
Jubilant Biosys Limited
08.2010 - 08.2018
- Published a work on building a classification model for blood brain barrier penetration.
- Built homology model of kinase DFG-out state and one of the GPCRs. The putative binding mode was predicted based on extensive docking and QM calculations. Compounds were evaluated and prioritized for the synthesis. Model was quite well in differentiating active and inactive molecules.
- For one of the client projects, predicted binding mode for the reference molecule was in very good agreement to the X-ray binding mode.
- For various drug discovery projects, suggested molecules based on protein active site were actives.
- Both ligand- and structure-based virtual screening was used in drug discovery projects to identify drug-like molecules. Ligand-based approaches included shape screening, similarity search, Pharmacophore screening and corehopping, whereas structure-based screening included docking, ensemble docking, E-pharmacophore model and core hopping. The selected compounds were purchased and 12% compounds showed >35% inhibition at 10µM. For one of the projects, the iterative process of ligand-based virtual screening led to the identification of novel scaffolds as well as the ideas for modifications to the core for improved activity.
- Theoretical study using quantum calculations was conducted to study the reaction mechanisms.
- Also worked on PPIs. Suggested one of the peptide constructs showed >30% inhibition.
Education
M.Tech -
SASTRA University
Thanjavur, India 04.2001 -
Master of Science -
Banaras Hindu University
Varanasi, India 04.2001 -
Skills
CompChem suite: ICMPro, Schrodinger, Cresset, MOE
Chemoinformatics: Chemaxon (IJC), Chemoffice, ISIS/MDL, CimPl, MarvinView
Molecular dynamics: GROMACS, Desmond, Amber
Publications
Singh M., Divakaran R., Konda LSK., Kristam R., A classification model for blood brain barrier penetration. J Mol Graph Model. 2020 May;96:107516. doi: 10.1016/j.jmgm.2019.107516. Epub 2019 Dec 20. PMID: 31940508.
Kannt, A. et al., A small molecule inhibitor of Nicotinamide N-methyltransferase for the treatment of metabolic disorders. Sci Rep 8, 3660 (2018).
Ruf S et al., Novel nicotinamide analog as inhibitor of nicotinamide N-methyltransferase. Bioorg Med Chem Lett. 2018 Mar 1;28(5):922-925.
Mathivanan, S.; Chunchagatta L., Puneeth Kumar ; Singh, M.; Giridharan, S.; Sathish, K.; Bharatham, K.; Kamariah, N., Structure of a 14-3-3 : FOXO3a phosphopeptide complex reveals 14-3-3 isoform specific binding of FOXO phosphoproteins. ACS Omega. 2022 Jul 5;7(28):24344-24352.
Singh, M.; Kempanna, P.; Bharatham, K. Identification of Mtb GlmU Uridyltransferase Domain Inhibitors by Ligand-Based and Structure-Based Drug Design Approaches. Molecules 2022, 27, 2805.
Accomplishments
Received "Individual Excellence Award" (2022) at APSL for successfully completing and delivering various client-based projects.
Received "Team Excellence Award (2023)" at APSL for contributing towards various CADD projects.
Received "Team Excellence Award (2024)" at APSL for contributing towards AILDD platform.
Topper in M.Tech (2010).
Received “Spot award” in Jubilant Biosys (2011) for consistent & effective support for client- based and internal discovery projects.
Received “Most Engaged Associate” award in Jubilant Biosys (2014) for consistent & effective support for client-based and internal discovery projects.
Been part of the “Best team award (2015)” for the contributions made to the internal project.
Been part of two “Best team awards” (2016) in recognition of the contribution towards client projects. Been part of the “BRD4” project which has been out-licensed to Checkpoint Therapeutics.
Timeline
Scientist
Aurigene Pharmaceutical Services Limited, APSL
03.2022 - Current
Project Scientist I
CCBT, InStem, NCBS
09.2018 - 03.2022
Sr. Research Associate
Jubilant Biosys Limited
08.2010 - 08.2018
M.Tech -
SASTRA University
04.2001 -
Master of Science -
Banaras Hindu University
04.2001 -
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