PROFILE

An organized and detail-oriented biologist with 12 years of experience in design and development of vaccine and small molecule inhibitors against human diseases.

An accomplished researcher with extensive skills in structure biology, biophysics, biochemistry molecular biology, design and development of functional assays, animal studies, as evident by 1 US Patent application, 14 peer-reviewed publications, 1 book chapter and 5 research/travel grants.

A recognized scientist with profound analytical and communication skills to contribute to scientific communities as an invited reviewer to evaluate 47 research publications for 18 peer-reviewed journals, editor in 2 scientific journals, and judge to evaluate research work of fellow students in 4 scientific proceedings.

PROFESSIONAL EXPERIENCES

Postdoctoral Research Experiences Dec 2016-current

The Toila lab, NIAID, NIH, Bethesda (previously at Washington University in St. Louis)

Established the mechanisms of tetracycline inactivation by solving crystal structures of novel 10+ tetracycline-inactivating enzymes, including Tet(X7) and Tet_HMM(4), led to 5+ publications.

Pioneered liver-stage-development assay and liposome-disruption-assay in the Tolia lab for testing the efficacy of different malaria immunogens, resulted in a reduction of expenditure, and the experimental time by 70%, and led to 1 US Patent and 3+ publications.

Identified 16 malaria antigens using bioinformatics tools that headed 4 significant projects in the lab broadening the research field of malaria vaccinology and resulted in a US patent application, and 2+ foreseen publications.

Revised and edited 3 R01 grants of the lab that included biophysical, cellular, and immunological studies of malaria antigens, and structural details of antibiotic inactivating enzymes.

Doctor of Philosophy (Ph. D.), Biological Sciences Aug 2009-Oct 2016

Indian Institute of Technology Delhi (IITD), Delhi, India;

University of Heidelberg, Germany

Identified 43 drug- and 10 vaccine-candidate against malaria using bioinformatics tools that led to a successful international grant application, and a multipronged approach to develop malaria therapeutics and resulted in 1 peer-reviewed publication.

Investigated LISP2 as a vaccine candidate and dUTPase and AP4AH enzymes as a therapeutic drug target against malaria using reverse genetics, animal, and insect studies that resulted in 2 high impact publications.

Secured 4 collaborative projects and co-supervised two Ph.D. students in computer-aided-drug-design, and acquired 6 co-authored publications.

M. S. (Pharm), Pharmacoinformatics Jun 2007-Jul 2009

National Institute of Pharmaceutical Education and Research (NIPER) Mohali, India

Analyzed root causes for the toxicity of market-withdrawn aldose reductase inhibitors using chem-bioinformatics techniques and designed twenty novel and safe inhibitors that resulted in a 1st author publication.

Established a collaborative project on diabetic cardiomyopathy targeting PKCβII enzyme using a ligand-based-drug-design approach and secured one 1st author publication.

EDUCATION

Doctor of Philosophy (Ph. D.) in Biological Sciences Aug 2009-Oct 2016

Kusuma School of Biological Sciences

Indian Institute of Technology Delhi (IITD), Delhi, India

University of Heidelberg, Germany

Advisors: Profs. James Gomes, B. Jayaram, and Fredrich Frischknecht

M. S. (Pharm) Pharmacoinformatics Jun 2007-Jul 2009

National Institute of Pharmaceutical Education and Research (NIPER) Mohali, India

Advisor: Dr. M. Elizabeth Sobhia

Bachelor of Pharmacy Aug 2003-May 2007

Delhi Institute of Pharmaceutical Sciences and Research

University of Delhi, Delhi India

AWARDS, HONORS, and FELLOWSHIPS

Awarded grant money from the National Institute of General Medical Sciences to attend the "X-Ray Methods in Structural Biology" course, Cold Spring Harbor, Oct 2019.

Best poster awardee at the 27th Meeting, German Society of Parasitology, Mar 2016.

Ph.D. Fellowships:

Heidelberg University Fellowship, Germany [Jan 2014-Apr 2014, Aug 2014-Dec 2014, Oct 2015-Nov 2016].

German Academic Exchange Service (DAAD), Germany [Jul 2012-Dec 2013]

Ministry of Human Resource Development (MHRD) Fellowship, India. [Aug 2009-Jun 2012, Jan 2015-June 2015].

Young Scientist International Travel Award (Dept. of Science and Technology), India. [Sep 2012].

International Travel Award (Immunology Foundation), India. [Sep 2012]

International Travel Award (Indian Council of Medical Research), India. [Sept 2012] (awarded but not availed).

M.S. (Pharm.) Fellowship

Ministry of Human Resource Development (MHRD) Fellowship, India [2007-2009] after qualifying the following entrance exams:

i.Graduate Aptitude Test in Engineering (GATE) (Pharmaceutical Science). All India Rank 431, Apr 2007.

ii.National Institute of Pharmaceutical Education and Research (NIPER) entrance exam, All India Rank 36, May 2007.

Media coverage: ScienceDaily; Washington University in St. Louis (WashU) Newsletter; Drew Reports Online; The Healthsite.com; SpaceForce; Phys.org; FlipBoard

SKILLS

Protein crystallization: Screening therapeutic proteins in hundreds of buffer conditions to obtain high-quality protein crystals using the hanging-drop method, micro-seeding crystal harvesting, soaking to co-crystallize protein-inhibitor complexes, hands-on experience with the liquid-handling robot and protein crystallization nano-drop robot.

Elucidation of protein crystal structures: X-ray crystallography, online data collection on different synchrotrons, data processing and solving the phase issue using molecular replacement (MR), single anamolous diffraction (SAD), and multiple anamolous diffraction (MAD).

Protein engineering: elimination of decoy epitopes in therapeutic proteins by resurfacing through thermostabilization, enhancing the efficacy of therapeutic enzymes, and understanding the dynamics of therapeutic proteins by molecular dynamics simulations, humanization of antibodies

Design and development of subunit vaccines: Heterologous expression of therapeutic antigens in E. coli and mammalian cells (HEK293), protein refolding from inclusion bodies, testing physical and chemical stability of therapeutic proteins, purification, characterization using thermostability assay, bio-layer interferometry (BLI), small-angle x-ray scattering (SAXS), asceptic preparation of sterile dosage forms.

Genetic manipulation: genetic manipulation of a pathogen to generate chimeric-, knockout-, or tagged-parasite lines. Phenotypic characterization of mutant parasites using mosquitoes and animal studies.

Design and development of in-vitro and in-vivo functional assays: high-throughput assays to study biological formulations and their stabilities such as liposome-disruption-assay, Plasmodium liver-stage-development assay, growth inhibitory assays, enzyme kinetics, enzyme inhibition, ELISA, fluorescent-based assays, and neutralization assays.

Animal studies: Blood withdrawal (retro-orbital bleed, tail bleed, cardiac blood collection), injections (intravenous, intramuscular, subcutaneous, intraperitoneal), dissections (open abdominal and thoracic cavities, splenectomy, isolate ileum, jejunum, cardiac puncture, isolate and process different tissues including liver, lung, and spleen), plasma separation, anesthetics and euthanasia (cervical dislocation, cardiac puncture), bioassay of acetylcholine using rat ileum, effect of physostigmine and atropine on drug response curve of acetylcholine, anticonvulsant activity (chemically induced seizure and rotarod test), evaluation of investigational malaria vaccine (genetically attenuated and subunit) in mice.

Insectary: Breeding Anopheles mosquitoes (up to 10,000 new mosquitoes per week) for product research and development. Picking pupae out of a dish of water, maintaining different life stages of mosquito: eggs, larvae, pupae, and adults. Feeding mosquitoes sugar water, pulverized fish food, and human blood. Examining disease transmission dynamics at the mosquito bite site that can influence infection outcome. Dissection to isolate mid-guts, haemolymph, and salivary glands.

Blood and plasma-derived biologics: Blood culture to grow malaria parasites, immunization of mice with infected blood from the donor mouse that was previously infected with attenuated malaria parasites. Separation of blood and serum and evaluation of immunogenicity of isolated serum in different in vitro and in vivo experiments.

Microbiology: Liquid and solid culture of bacteria, isolation, and characterization of bacteria. Isolation of genomic DNA, RNA, and plasmid DNA, plasmid curing, site-directed mutagenesis, DNA gel analysis, quantification and extraction and molecular cloning techniques such as primers design, amplification of DNA by PCR, restriction enzyme digestion, ligation, bacterial transformation, colony PCR, cell culture.

Analytical techniques: SDS-PAGE, western blot, titrations, chromatography (ion exchange, gel exclusion, reverse phase, affinity, HPLC, FPLC), Spectroscopy (Circular Dichroism, Intrinsic and extrinsic Fluorescence, and UV-Visible), negative-stain transmission electron microscopy (TEM), biolayer interferometry (Octet RED96e System), light and fluorescent microscopy, liquid-handling robots, nanodrop, quality assurance, process automation, laboratory operation under GLP guidelines including SOPs.

Computer-aided drug design: Homology modeling, molecular docking, quantitative structure-activity relationship (QSAR), pharmacophore mapping, molecular dynamics, and high throughput virtual screening.

Computational skills

Software

Computer-aided-drug design: Schrodinger, MODELLER, Discovery studio, Avogadro, Autodock, Pymol, Rasmol, Amber, Gromacs, VMD, Chimera, ChimeraX, LIGPLOT, OpenBabel

Crystallography: XDS, XDSGUI, Phenix, Coot, adxv, CCP4, HKL2000, Molprobity

Protein design: Rosetta, Bioluminate

Image analysis: ImageJ, Fiji, Volocity, Adobe Photoshop, Adobe Illustrator

Cryo-EM: cryoSPARC, Rossetta, RELION

Bioinformatics: BLAST, Clustal Omega, Espript, T-Coffee, PROCHECK, Snapgene,

Statistics: Prism, MS Excel, Gnuplot

Programming language: Python, Shell script, R

Operating systems: Linux, Macintosh, Window

PROFESSIONAL SERVICES

Scientific Editor

Review Editor in Frontiers in Cellular and Infection Microbiology (section: Clinical Microbiology)

EC Microbiology

International Journal of Bioinformatics and Biological Sciences

Fellow Editorial Board (FEB), a free and confidential scientific document editing service of the NIH, that edits, and improvises other postdoctoral fellows' manuscripts for grammar, clarity, and information flow.

Lead judge

Lead judge to evaluate the posters of post baccalaureates at NIH Bethesda during Postbac Poster Day, 2019.

Judge to evaluate postdoctoral fellows' posters submitted to "The Fellows Award for Research Excellence (FARE), 2021.

Organizer

Coordinated and organized career-panels on federal jobs and evaluated post baccalaureates' scientific posters in 13th National Institute of Allergy and Infectious Diseases (NIAID) Fellow Workshop as a member of the National Institute of Allergy and Infectious Diseases (NIAID) Fellows Advisory Committee (FAC).

Coordinated and organized postdoctoral fellow weekly meetings to discuss an assortment of original and exemplary research papers, 2019.

Mentions in press

My approach to get a job at FDA (Center for Cancer Research Fellows and Young Investigators (CCR-FYI) newsletter)

Postdoc-spotlight-networking-new-skills-and-next-steps (National Institute of Allergy and Infectious Diseases (NIAID) newsletter)

Reviewer (Publons profile)

Elsevier certified reviewer and have reviewed 48 research articles for following publishing groups (total number of reviewed articles):

American Society for Microbiology: Infection and Immunity (2)

BioMed Central: BMC Veterinary Research (3); Malaria (in the supervision of PI) (1)

Dove Press: Journal of Experimental Pharmacology (1); International Journal of Nanomedicine (1)

Elsevier: Infection, Genetics and Evolution (3); Molecular and Biochemical Parasitology (3); Bioorganic & Medicinal Chemistry (1); Bioorganic Chemistry (1)

Frontiers: Frontiers in Oncology (1); Frontiers in Cell and Developmental Biology (1); Frontiers in Cellular and Infection Microbiology (6)

Multidisciplinary Digital Publishing Institute: Genes (1); Microorganisms (3)

Omics International: Pharmaceutica Analytica Acta (3)

Peer Journals: The Journal of Life and Environmental Sciences (2)

PLoS: PLoS One (1)

Society for Imaging Science and Technology: Journal of Imaging Science and Technology (1)

Taylor and Francis Online: Journal of Biomolecular Structure and Dynamics (7)

Willey: Journal of Applied Microbiology (1)

Memberships

American Society of Tropical Medicine and Hyegine, 2019-2020.

The Antibody Society, 2020-2022.

Indian Pharmaceutical Graduate Association, Life-time member

Registered Pharmacist, Delhi Pharmacy Council (Registration no.-19446).

American Medical Writing Association, 2020-2021.

WORKSHOPS/COURSES/PROCEEDINGS

"X-Ray Methods in Structural Biology." Cold Spring Harbor, Oct 2019.

"Cryo-EM Workshop 2019" on Image processing. University of Michigan, Jun 2018

"Animal Handling Course." Federation for Laboratory Animal Science Associations (FELASA), University of Heidelberg, Germany. Feb 2013.

"Protein: Structure, Function, and Folding" Indian Institute of Science, Bangalore, India. Dec 2010.

"Molecular biology: a laboratory training course." B. V. Patel PERD Centre, Ahmedabad, India. Jun 2010.

"In vitro culture of malaria parasites." National Institute of Malaria Research, New Delhi, India. Jun 2010.

"SERC summer school in modeling and informatics in drug design" NIPER, Mohali, India. Jul 2007.

"Workshop on Pharmacoinformatics: Structure-based-drug-design" NIPER, Mohali, India. Mar 2008.

Industrial training (parenteral, production, and quality control units). Albert David Limited, Ghaziabad, India. Jun 2007.

Course undertaken during Ph.D. : Signaling pathways analysis, systems biology, advanced cell biology, biometry, chaperon and protein conformational disorders, protein aggregation and diseases, chemiinformatics and molecular modelling, graduate research seminar, biological membranes, communication skills.

Courses undertaken during M.S. (Pharm.) Pharmacoinformatics: Biostatistics, spectral analysis, basics of drug action, drug metabolism and toxicity and metabolic disorders, pharmacological screening and assays, informatics and informational technology, dosage form design parameters, pharmacokinetics and biopharmaceutics, molecular biology, genomics proteomics and systems biology, bioinformatics, drug design, structure and function of biomolecules, pharmacoinformatics-the tools, pharmacoinformatics-the methodology, pharmacy informatics, intellectual property right.

Courses undertaken during B. Pharm: Pharmacology, human anatomy physiology and health education, pathophysiology and toxicology, hospital pharmacy, pharmaceutical jurisprudence, pharmaceutical biotechnology, pharmaceutical microbiology including biological pharmacy, biopharmaceutics and clinical pharmacy, dosage form design, biochemistry, organic chemistry, physical chemistry, pharm. inorganic chemistry, physical pharmacy, medicinal chemistry, chemistry of natural products, pharmacognosy, pharmaceutical analysis, pharmaceutical technology, engineering drawing, pharmaceutical engineering, dispensing and community pharmacy, pharmaceutical management and professional pharmacy, mathematics, basics electronics and computer.

BIBLIOGRAPHY

Patent

PCT application on Malaria immunogen, antibodies, and method of their usage thereof. (Country: USA). Application # US20190276506A1.

Project grants

Independent grant application

"Role of Autophagy in Pancreatic Cancer Progression" submitted as a chief investigator (CIE) to National Health and Medical Research Council (NHMRC), Australia.

The reviewing committee has evaluated the grant application, and the grant has been advanced for resubmission.

In the supervision of PIs

"Identification of drugs- and druggable-targets for Malaria" sanctioned by DAAD, India (Feb 2012) (funded Ph.D. research for 1.25 years in Heidelberg, Germany).

"Computer-aided-drug-design of Selective and Specific Aldose Reductase (ALR2) Inhibitors for the Treatment of Diabetic Complications" sanctioned from Council for Scientific and Industrial Research (CSIR, India) during MS (Pharm.) (Total grant: ~ $40 000).

Publications (Link to Google scholar, Orcid, Linkedin profiles)

15. Sharma V, Wakode S, Kumar H. Structure- and Ligand-based Drug Design: Concepts, Approaches and Challenges. (Invited Book Chapter, Elsevier; in Revision)

14. Gasparrini D, Markley J, Kumar H, Wang B, Irum S, Wallace M, Burnhamm D, Andleeb S, Tolia H N, Wencewicz T, Dantas G. Tetracycline resistance by inactivation across environmental, human commensal, and pathogenic microbes. Communications Biology 2020 (PMID: 32415166)

13. Moreau C A, Quadt K A, Piirainen H, Kumar H, Bhargav S P, Strauss L, Tolia N H, Wade R C, Spatz J P, Kursula I, Frischknecht F. A function of profilin in force generation during malaria parasite motility independent of actin-binding. Journal of Cell Science 2020 (PMID: 32034083)

12. Kumar H, Tolia H N. Getting in: the structural biology of malaria invasion. PLoS Pathogen, 2019 (Section: Pearl, Host-parasite-interactions) (PMID: 31487334)

11. Markley J, Fang L, Gasparrini D, Symister C, Kumar H, Tolia H N, Dantas G, Wencewicz T. Semisynthetic Analogues of Anhydrotetracycline as Inhibitors of Tetracycline Destructase Enzymes. ACS Infectious Diseases 2019 (PMID: 30835428)

10. Kumar H, Kehrer J, Singer M, Reinig M, Santos M J, Mair G, Frischknecht F. Functional genetic evaluation of DNA house-cleaning enzymes as malaria drug targets: dUTPase and, Ap4AH are essential in Plasmodium berghei but ITPase, NDH is not. Experts Opinions On Therapeutic Targets 2019 (PMID: 30700216)

9. Douglas R, Nandekar P, Aktories J, Kumar H, Weber R, Singer M, Lepper S, Sadiq K, Wade R.2, and Frischknecht F. Inter-subunit interactions drive divergent dynamics in mammalian and Plasmodium actin filaments. PLoS Biology 2018 (PMID: 30011270)

8. Santos J M, Egarter S, Zuzarte-Luís V, Kumar H, Moreau CA, Kehrer J, Pinto A, Costa M D, Franke-Fayard B, Janse C J, Frischknecht F, Mair GR. Malaria parasite LIMP protein regulates sporozoite gliding motility and infectivity in mosquito and mammalian hosts. eLife 2017 (PMID: 28525314)

7. Moreau C A, Bhargav S P, Kumar H, Quadt K A, Piirainen H, Strauss L, Kehrer J, Streichfuss M, Spatz J P, Wade R C, Kursula I, Frischknecht F. A unique profilin-actin interface is important for malaria parasite motility. PLoS Pathogens 2017 (PMID: 28552953)

6. Sharma V, Kumar H, Wakode S. Pharmacophore generation and atom-based 3D-QSAR of quinoline derivatives as selective phosphodiesterase 4B inhibitors. RSC Advances 2016 (DOI: 10.1039/C6RA11210B)

5. Kumar H, Sattler J M, Singer M, Heiss K, Ester M, Hammerschmidt-Kamper K, Heussler V, Mueller A K and Frischknecht F. Inverse relation of protective efficacy and safety in attenuated malaria parasites lacking two liver stage-specific proteins LISP2 and UIS3. Scientific Reports 2016 (PMID: 27241521)

4. Kumar H, Frischknecht F, Mair GR and Gomes J. In silico identification of genetically attenuated vaccine candidate genes for Plasmodium liver stage. Infection Genetics and Evolution 2015 (PMID: 26348884)

3. Padhi AK, Kumar H, Vasaikar SV, Jayaram B, Gomes J. Mechanisms of loss of functions of human angiogenin variants implicated in amyotrophic lateral sclerosis. PLoS One 2012 (PMID: 22384259)

2. Kumar H, Shah A, Sobhia ME. Novel insights into the structural requirements for the design of selective and specific aldose reductase inhibitors. Journal of Molecular Modeling 2012 (PMID:21833829)

1. Kumar H, Kumar R, Grewal BK, Sobhia ME, Insights into the structural requirements of PKCβII inhibitors based on HQSAR and CoMSIA analyses. Chemical Biology and Drug Design 2011 (PMID: 21605345)

Manuscript (in review)

16. Kumar H, Jimah R J, Schlesinger H P, Tolia H N. CelTOS pore-forming domains exposed: From lipid binding, conformational flexibility to regulatory regions.

(Two 1st author manuscripts are in preparation)

Presentations

Oral presentations

"CelTOS domains exposed: From lipid binding, conformational flexibility to regulatory regions." MPIG and SBIG Student and Postdoc Symposium, NIH Bethesda, the USA. April 2019.

"Tweaking the silent stage of the parasite." Intracellular Niches of Pathogens. Frankfurt, Germany. October 2013.

"Comparative molecular dynamics simulations study of PfFabI inhibitors." MolMod2011, Heidelberg, Germany. October 2011.

Poster presentations

"CelTOS domains exposed: From lipid binding, conformational flexibility to regulatory regions." American Society of Tropical Medicine and Health, Nov 2019.

"Genetic manipulations to develop a liver-stage attenuated malaria vaccine." 27th Meeting, German Society of Parasitology, Göttingen, Germany. Mar 2016 (Best poster award)

"Comparative molecular dynamics simulations study of PfFabI inhibitors." MolMod2011, Heidelberg, Germany. Oct 2011.

"A molecular dynamics simulation study of PfApiAP2". Nucleic Acids in Disease and Disorders. IIT Delhi, New Delhi, India. Dec 2011.

"Insight into the structural requirement for PKCβII inhibition by CoMSIA and HQSAR studies." Indian Pharmaceutical Conference. New Delhi, India. Dec 2008.

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