Amit Kumar Chaudhary, Ph.D.

AMIT K. CHAUDHARY, Ph.D.

510 S. 39th Street Apt#31 Omaha, NE 68105

amitkumarchaudhary3@gmail.com +1-402-203-9777

Summary of Achievements:

• Characterized negative regulator doxR gene using antisense RNA from doxorubicin producing Streptomyces peucetius and deposited the sequence to GenBank.

• Designed and constructed multi-monocistronic expression vector for Streptomyces and used it for the expression of antisense RNAs for silencing doxR gene to enhance doxorubicin production.

• Designed and constructed tightly regulated expression vector for Escherichia coli and biotransformation of therapeutic small molecule.

• Engineered Escherichia coli to produce 2-deoxystreptamine (2-DOS), flavonol glycosides, enhanced production of nargenicin A1 and create its novel derivative.

• Developed novel hedgehog Inhibitor, which has better therapeutic activity for pancreatic cancer compared to FDA-approved GDC-0449.

• In overall, I have been working in the field of natural product combinatorial biosynthesis, synthetic biology, and drug discovery to find a new way to treat human diseases.

Industrial experience:

• 03/01/2009-05/31/2009: Worked as intern in Everest Biotech Pvt. Ltd (http://everestbiotech.com/), a specialist in goat polyclonal antibodies producing company in Nepal. During this period, I worked on preparation of immunogen from peptide antigens, serum processing and IgG precipitation, affinity purification, ELISA, SDS-PAGE, and Western Blot.

Patent:

• Construction of a multi-monocistronic vector applicable for synthetic biology and use thereof (http://worldwide.espacenet.com/publicationDetails/biblio?FT=D&CC=KR&NR=20140042398A)

Submitted nucleotide sequence of doxR in GenBank:

• DoxR from Streptomyces peucetius ATCC 27952, complete cds, GenBank: JQ814785.1. Hands-on experiences: ➢ Molecular Biology Techniques:

• PCR, qRT-PCR, cloning, expression and purification of recombinant proteins.

• SDS-PAGE, Western bolt, ELISA, estimation of nucleic acids and proteins.

• Designing and constructions of expression vectors for large-scale assembly of genes in monocistronic fashion.

• Handling, maintenance, and metabolic engineering of Streptomyces, Escherichia coli, and Methanotrophs.

• Handling and maintenance of mammalian cell culture, transfection and transduction of nucleic acids. MTT assay, apoptosis, cell cycle, cell invasion, and migration assays.

• Handling and maintenance of mouse models.

• Generation of orthotopic and subcutaneous tumor mouse models.

• Spectrophotometry and chromatography like TLC, HPLC, and FACS analysis.

Amit Kumar Chaudhary, Ph.D.

➢ Bioinformatic tools:

• BLAST (protein, nucleotide), multiple sequence alignment, chembiodraw, primer designing.

Education:

• 2014: Doctor of Philosophy in Biochemistry (Ph.D), Sun Moon University, Republic of Korea.

• 2008: Master of Science in Biotechnology (M.Sc), University of Mysore, Mysore, India.

• 2005: Bachelor of Science in Microbiology/Genetics (B.Sc), Nizam College (Autonomous), A constituent College of Osmania University, Hyderabad, India.

Research experience:

• 05/01/2015-Present: Postdoctoral Research Associate: University of Nebraska Medical Center, Omaha, NE, USA.

• 09/01/2014-02/28/2015: Postdoctoral Research Associate: Kyung Hee University, Yongin, Republic of Korea.

• 08/01/2008-02/28/2009: Volunteer: Biotechnology Unit, Nepal Agricultural Research Council, Nepal. http://narc.gov.np/narc/index.php.

• 03/15/2008-05/05/2008: Project: Dr. B.C. Guha Center for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India.

Peer-reviewed articles:

• A.K.Chaudhary, R.S.Bhattarai, R.I.Mahato; The fourth annual BRDS on genome editing and silencing for precision medicines. Drug Delivery and Translational Research (2017), DOI: 10.1007/s13346-017-0457-5.

• G.Mondal, S.Almawash, A.K.Chaudhary and R.I.Mahato; EGFR-Targeted Cationic Polymeric Mixed Micelles for Codelivery of Gemcitabine and miR-205 for Treating Advanced Pancreatic Cancer. Molecular Pharmaceutics (2017) 5;14(9):3121-3133.

• A.K.Chaudhary, G.Mondal, R.I.Mahato et al; Chemosensitization and inhibition of pancreatic cancer stem cell proliferation by overexpression of microRNA-205. Cancer Letters (2017) 402:1-8.

• V.Kumar,# A.K.Chaudhary,# R.I.Mahato et al; Design, Synthesis and Biological Evaluation of novel Hedgehog Inhibitors for treating Pancreatic Cancer. Scientific Reports (2017) 10;7(1):1665. # Equal contribution.

• A.K.Chaudhary and R.I.Mahato; The third annual BRDS on research and development of nucleic acid-based nanomedicines. Drug Delivery and Translational Research (2016), DOI: 10.1007/s13346-016-0345-4.

• D.Dhakal, A.K.Chaudhary, J.K.Sohng et al; Enhanced production of nargenicin A1 and creation of a novel derivative using a synthetic biology platform. Applied Microbiology and Biotechnology (2016), DOI: 10. 1007/s00253-016-7705-3.

• A.R.Pokhrel, A.K.Chaudhary, J.K.Sohng et al; Overexpression of a pathway specific negative regulator enhances production of daunorubicin in bldA deficient Streptomyces peucetius ATCC 27952. Microbiological Research (2016), DOI: 10.1016/j.micres.2016.06.009.

• D.Wen, M.Danquah, A.K.Chaudhary and R.I. Mahato; Small molecules targeting microRNA for cancer therapy: promises and obstacles. Journal of Controlled Release (2015), DOI: 10.1016/j.jconrel.2015.08.011.

• A.K.Chaudhary and E.Y.Lee; Tightly regulated and high-level expression vector construction for Escherichia coli BL21 (DE3). Journal of Industrial and Engineering Chemistry (2015), DOI: 10.1016/j.jiec.2015.07.011.

• A.K.Chaudhary, A.R.Pokhrel, J.K.Sohng et al; Paired-termini antisense RNA mediated inhibition of DoxR in Streptomyces peucetius ATCC 27952. Biotechnology and Bioprocess

Amit Kumar Chaudhary, Ph.D.

Engineering 20: 381-388 (2015), DOI: 10.1007/s12257-014-0810-1.

• P.Parajuli, R.P.Pandey, N.T.H.Trang, A.K.Chaudhary and J.K.Sohng; Synthetic sugar cassettes for the efficient production of flavonol glycosides in Escherichia coli. Microbial Cell Factories (2015), DOI: 10.1186/s12934-015-0261-1.

• A.K.Chaudhary, D.Na and E.Y.Lee; Rapid and high-throughput construction of microbial cell-factories with regulatory noncoding RNAs. Biotechnology Advances (2015), DOI: 10.1016/j.biotechadv.2015.05.009.

• A.K.Chaudhary, I.Y.Hwang, E.Y.Lee et al; Enzymatic synthesis of amentoflavone glycoside using recombinant oleandomycin glycosyltransferase. Journal of Industrial and Engineering Chemistry 25 (2015), DOI: 10.1016/j.jiec.2014.11.008.

• A.K.Jha, A.R.Pokhrel, A.K.Chaudhary, J.K.Sohng et al; Metabolic engineering of rational screened Saccharopolyspora spinosa for enhancement of spinosyns A and D production. Molecules and Cells (2014), DOI: 10.14348/molcells.2014.0168.

• A.K.Chaudhary, B.Singh, J.K.Sohng et al; Switching antibiotics production on and off in Actinomycetes by an IclR family transcriptional regulator from Streptomyces peucetius ATCC 27952. Journal of Microbiology and Biotechnology (2014), DOI: 10.4014/jmb.1403.03026.

• A.K.Chaudhary, D.Dhakal and J.K.Sohng; An insight into the omics based engineering of Streptomycetes for secondary metabolite overproduction. BioMed Research International (2013), DOI.org/10.1155/2013/968518.

• A.K.Chaudhary, J.W.Park, J.K.Sohng et al; Re-engineering of genetic circuit for 2-deoxystreptamine (2-DOS) biosynthesis in Escherichia coli BL21 (DE3). Biotechnology Letters (2013), DOI 10.1007/s10529-012-1077-2.

• A.K.Chaudhary, A.R.Pokhrel, J.K.Sohng et al; Bioinformatic analysis of T1pks-T3pks-nrps, a PKS and NRPS hybrid pathways from complete genome of Streptomyces venezuelae ATCC 10712. Journal of Biomolecule Reconstruction (2013), http://smibr.co.kr/bbs/data/sub31/JBR_2013_1_1.Amit.pdf.

• N.H.Hoang, A.K.Chaudhary, J.W.Park et al; Cloning and expression of the second glycosyltransferase gene - kanM2 of kanamycin biosynthetic gene cluster in Escherichia coli BL21 (DE3). Journal of Biomolecule Reconstruction (2013), http://smibr.co.kr/bbs/data/sub31/JBR_2013_1_5.Hoang.pdf.

• D.Dhakal, A.K.Chaudhary, J.K.Sohng et al; Underpinning the secondary metabolites from Nocardia spp. Journal of Biomolecule Reconstruction (2013); http://smibr.co.kr/bbs/data/sub31/JBR_2013_1_2.Dipesh.pdf.

• A.R.Pokhrel, A.K.Chaudhary, J.K.Sohng et al; Cloning of two initial genes of synthetic epothilone biosynthetic gene cluster for transcript analysis and protein expression. Journal of Biomolecule Reconstruction (2013); http://smibr.co.kr/bbs/data/sub31/JBR_2013_1_9.Anaya.pdf.

• A.R.Pokhrel, A.K.Chaudhary and J.K.Sohng; New antibiotics as an emerging need and an enormous challenge. Journal of Biomolecule Reconstruction (2012), http://smibr.co.kr/bbs/data/sub31/2012_2_1_anaya.pdf.

• A.K.Chaudhary, N.T.L.Huong, J.K.Sohng et al; Codon optimized expression of difficult to express first glycosyltransferase enzyme of kanamycin and neomycin biosynthetic pathway in Escherichia coli. Journal of Biomolecule Reconstruction (2012); http://smibr.co.kr/b bs/data/sub31/2012_2_3Amit.pdf.

• A.K.Chaudhary, A.R.Pokhrel, J.K.Sohng et al; tRNA encoding for a rare leucine codon, UUA may enhance doxorubicin production in Streptomyces peucetius ATCC 27952. Journal of Biomolecule Reconstruction (2011); http://smibr.co.kr/bbs/data/sub31/JBR_2011_2_3.Amit.pdf.

• A.K.Chaudhary, A.R.Pokhrel, J.K.Sohng et al; Monocistronic approach using synthetic biology for microbial system re-engineering. Journal of Biomolecule Reconstruction (2011); http://smibr.co.kr/bbs/data/sub31/4._Amit.pdf.

• A.K.Chaudhary, N.P.Niraoula, J.K.Sohng et al; Phenotypic characterization of apramycin N (3)-

Amit Kumar Chaudhary, Ph.D.

acetyltransferase IV resistance gene from Streptomyces kanamyceticus ATCC12853. Journal of Biomolecule Reconstruction (2010); http://smibr.co.kr/bbs/data/sub31/1.Amit_BR_2010_2.pdf.

Conference abstracts:

• A.K.Chaudhary, K.Kattel, R.I.Mahato; A therapeutic approach to treat chemoresistant pancreatic cancer using miR-205 and gemcitabine. 13–17 November 2016 AAPS Annual Meeting and Exposition; Colorado Convention Center; Denver, USA.

• V.Kumar, V.Kumar, A.K.Chaudhary, R.I.Mahato et al; Synthesis and nano-formulation of potent analogues of GDC-0449, a hedgehog inhibitor for the treatment of pancreatic cancer. 3rd Annual Biopharmaceutical Research and Development Symposium; 14-15 September 2016, University of Nebraska Medical Center, USA.

• A.R.Pokhrel, A.K.Chaudhary, J.K.Sohng et al; Overexpression of a pathway specific self-repressing regulator enhances production of daunorubicin in bldA deficient Streptomyces peucetius ATCC 27952. 43rd KMB Annual Meeting & International Symposium, 2016.

• B.Shrestha, A.K.Chaudhary, J.K.Sohng et al; Exploring the role of CYP 450 (Orf20) in clavulanic acid production in Streptomyces clavuligerus NRRL 3585. 2014 The Korean Society for Biotechnology and Bioengineering Fall Meeting & International Symposium; 5~7 October 2014 CECO; Republic of Korea.

• S.Darsandhari, N.Koirala, A.K.Chaudhary and J.K.Sohng; Methylation of selected flavonoids in vitro using O-methyltransferase from Streptomyces kanamyceticus. 2014 The Korean Society for Biotechnology and Bioengineering Fall Meeting & International Symposium; 5~7 October 2014 CECO; Republic of Korea.

• A.R.Pokhrel, T.V.Duong, R.P.Pandey, A.K.Chaudhary, J.K.Sohng et al; An attempt to enhance the solubility of violacein by generating glycoside analogs. 2014 The Korean Society for Biotechnology and Bioengineering Fall Meeting & International Symposium; 5~7 October 2014 CECO; Republic of Korea.

• H.T.Nguyen, A.K.Chaudhary, J.K.Sohng et al; Codon optimized expression of difficult to express first glycosyltransferase–KanF gene of Kanamycin biosynthetic pathway in E. coli. 2014 The Korean Society for Biotechnology and Bioengineering Fall Meeting & International Symposium; 5~7 October 2014 CECO; Republic of Korea.

• P.Parajuli, R.P.Pandey, N.T.Huyen Trang, A.K.Chaudhary and J.K.Sohng; Efficient sugar cassettes for the production of flavonol glycosides in Escherichia coli. 7th Copenhagen Bioscience Conference - a novo nordisk foundation initiative, 17-21 May 2015.

• D.Dhakal, A.K.Chaudhary, J.K.Sohng et al; Enhancement of nargenicin A1 using synthetic biological platform. KMB 2015 42nd Annual Meeting & International Symposium.

• A.R.Pokhrel, A.K.Chaudhary, J.K.Sohng et al; The bldA tRNA helps to enhance production of doxorubicin and its intermediates in Streptomyces peucetius ATCC 27952. KMB 2015 42nd Annual Meeting & International Symposium.

• A.K.Chaudhary, A.R.Pokhrel, J.K.Sohng et al; Engineering Escherichia coli BL21 (DE3) for biosynthesis of 1-deoxynojirimycin (DNJ) using single vector multi-modular system. 2014 KSBB Spring Meeting and International Symposium, 9-11 April, Hyundai Hotel, Gyeongju, Republic of Korea.

• A.K.Jha, A.R.Pokhrel, A.K.Chaudhary, J.K.Sohng et al; Metabolic engineering of rational screened Saccharopolyspora spinosa for enhancement of spinosyns A and D production. 2014 KSBB Spring Meeting and International Symposium, 9-11 April, Hyundai Hotel, Gyeongju, Republic of Korea.

• D.Dhakal, A.K.Chaudhary, J.K.Sohng et al; Construction of multi-monocistronic vector for Nocardia species. 2014 KSBB Spring Meeting and International Symposium, 9-11 April, Hyundai Hotel, Gyeongju, Republic of Korea.

• A.K.Chaudhary, I.Y.Hwang, E.Y.Lee et al; Enzymatic synthesis of amentoflavone glycoside

Amit Kumar Chaudhary, Ph.D.

using “OleD” glycosyltransferase from Streptomyces antibioticus. 2014 KSIEC Fall Meeting, Republic of Korea.

• A.K.Chaudhary, J.W.Park and J.K.Sohng; Re-engineering of genetic circuit for 2-deoxystreptamine (2-DOS) biosynthesis using single vector multi-monocistronic approach in Escherichia coli BL21 (DE3). 15th International Biotechnology Symposium and Exibition (IBS) 2012, 16-21 Sept, EXCO, Daegu, Republic of Korea.

Awards and extracurricular activities:

• Recognized at the 2017 UNeMed Research and Innovation Awards for disclosing an invention “Design, Synthesis and Evaluation of Novel Hedgehog Inhibitors for Treating Pancreatic Cancer” University of Nebraska Medical Center, October 26, 2017.

• CHC Scholarship Award for the academic excellence and contribution to the Institute of Biomolecule Reconstruction at Sun Moon University, 2011, Republic of Korea.

• Certificate of participation for poster presentation organized by University of Mysore, Mysore, 2007, India.

• Aid-Nepal silver jubilee scholarship for Master of Science (M.Sc) to study in University of Mysore by Embassy of India, Nepal, 2006.

• General cultural exchange scholarship for Bachelor of Science (B.Sc) to study in Nizam College (Autonomous) a constituent college of Osmania University b y Embassy of India, Nepal, 2002.

• International Coordination Council (2011-2015) of Worldwide Nepalese Students' Origination (WNSO), a non-political, non-profit making, organization that constitutes the Nepalese students and young professionals all over the world, Republic of Korea Chapter.

Members:

• Emergent Life Sciences Research (ELSR), Reviewer. http://www.emergentresearch.org/reviewer_board.php

• EC Microbiology (ECMI), Editorial Member. https://www.ecronicon.com/microbiology-editorial-panel.php

➢ EC Microbiology Editor’s Column: ▪ A.K. Chaudhary; Demanding Novel Tools for Engineering Streptomycetes. EC Microbiology

4.4 (2016): 720-721. ▪ A.K. Chaudhary; Synthetic Biology, A New Tool for Biological System Engineering

Discipline-An Overview. EC Microbiology ECO.01 (2016): 05-09.

• Scientia Ricerca, Clinical Biotechnology and Microbiology Journal, Editorial Member. https://scientiaricerca.com/cbmi-eb.php

• American Association for the Advancement of Science (AAAS) Member.

• American Association of Pharmaceutical Scientists (AAPS). I certify that all the information stated in this CV is true and complete to the best of my knowledge. Amit Kumar Chaudhary, Ph.D