Scientist Profile

Shailza Singh, Ph.D.

Email

singhs@nccs.res.in

Research Areas

Pathogenesis and Cellular Response

Education 

Ph.D.-Indian Institute of Technology, Delhi
M.Sc.-Banaras Hindu University, Varanasi

Research

Bioinformatics, Computational Structural Biology and Systems Biology

The lab focuses on molecular dynamics simulation of proteins and their interacting molecules. We have shown structural information about drug-protein complexes fundamental for drug discovery via virtual screening and how it guides the optimization of the pharmacological properties of these molecules. Lately, we have started working on systems biology where we aim to integrate the action of regulatory circuits, cross-talk between pathways and the non-linear kinetics of biochemical processes through mathematical models. The current thrust is to explore the possibility of network-based drug design and how rationalized therapies may benefit from Systems Biology.

Drug Delivery and Translational Research

The lab is focused on topics such as designing and developing novel drug delivery systems, nanomedicine; with a focus on their application to disease conditions; short-term and long-term biocompatibility of drug delivery systems, host response and devices for drug delivery and drug/device combination products.

LmSmdB Database

SBCdb Database

TryTransDB (NEW LINK)

Details of Projects under Implementation:

S.No. Title Duration Role as PI/Co-PI Agency
1. Delineating the relationship between mir146,lipid metabolism and autophagy in Leishmania : A Systems Perspective 2019-3999/CMB/BMS (2019-2022)16.8.2019-15.8.2022 PI ICMR

Details of the projects completed during the last five years:

S.No. Title Duration Role as PI/Co-PI Agency
1. Drug Target Identification in L.major and S.mansoni through Biochemical Network Modeling (2012-15)

 

20/6/2012-19/6/2015
PI DBT
2. Systems Biology of Metabolic Network of L.major: Therapeutic Implications (2012-15) 11/09/2012-10/9/2015 PI DBT
3. Systems and Synthetic Biology in Leishmania : A Bioinformatics Approach (2013-2016) 24/07/2013-23/07/2016 PI DST
4. Molecular motors as nanocircuits in Leishmaniasis : System cues guiding synthetic biology device construction   (2016-2019)(18.5.2016-17.5.2019) PI DBT
5. Understanding the mechanism of ABC-type metal sequestering proteins: structure-based novel drug development against human pathogens (2017-2020) 20.1.2017-19.7.2020)  Collaborating Institute PI DBT-Twinning Program for NE

List of  Selected Papers

Kabra R, Ingale P, Singh Shailza*. Computationally designed synthetic peptides for transporter proteins impart allostericity in Miltefosine resistant L. major. Biochem J. 2020 May 29; 477(10):2007-2026. Doi: 10.1042/BCJ20200176. PMID: 32391551.

Nimsarkar P, Ingale P, Singh Shailza*. (2020) Systems Studies Uncover miR-146a as a Target in Leishmania major Infection Model. ACS Omega. 2020 May 18.

Chauhan N, Singh Shailza*. (2020) Multiscale Process Modeling in Translational Systems Biology of L.major : A Holistic View. Scientific Reports  DOI: 10.1038/s41598-020-57640-4

Ingale P, Kabra R, Singh Shailza*. (2020) Structural sequence evolution and computational modeling approaches of the complement system in leishmaniasis. Adv Protein Chem Struct Biol. 2020;120:409-424. doi: 10.1016/bs.apcsb.2019.12.004. Epub 2020 Jan 10. PMID: 32085887

Chauhan N, Singh Shailza* (2019) Integrative Computational framework for Understanding Metabolic Modulation in Leishmania. Front. Bioeng. Biotechnol  doi: 10.3389/fbioe.2019.00336 PMID: 31803732

Kumar A, Chauhan N, Singh Shailza*. (2019) Understanding the Cross-Talk of Redox Metabolism and Fe-S Cluster Biogenesis in Leishmania through Systems Biology Approach. Front Cell Infect Microbiol. 2019 Feb 4; 9:15. doi: 10.3389/fcimb.2019.00015. eCollection 2019. PMID: 30778378

Mol M, Kosey D, Boppana R, Singh Shailza*. (2018) Transcription Factor Target Gene Network governs the Logical Abstraction Analysis of the Synthetic Circuit in Leishmaniasis. Sci Rep. 2018 Feb 22; 8(1):3464. doi: 10.1038/s41598-018-21840-w. PMID: 29472639

Pruthvi Raj B and Shailza Singh* (2018) Engineering riboswitch in L.major: From prediction to conceptualization. International Journal of Biological Macromolecules https://doi.org/10.1016/j.ijbiomac.2018.04.031PMID: 29655887

Soni B, Saha B, Singh Shailza*. (2017) Systems cues governing IL6 signaling in leishmaniasis. Cytokine. 2017 Nov 8. pii: S1043-4666(17)30343-5. doi: 10.1016/j.cyto.2017.11.001. [Epub ahead of print] PMID: 29128405

Vineetha Mandlik, Sohan Patil, Ramanamurthy Bopanna, Sudipta Basu and Shailza Singh* (2016) Biological activity of coumarin derivatives as antileishmanial agents. Plos One 10.1371/journal.pone.0164585

Singh Shailza*, Mandlik V, Shinde S. (2015) Molecular dynamics simulations and statistical coupling analysis of GPI12 in L. major: functional co-evolution and conservedness reveals potential drug-target sites. Mol Biosyst. 2015 Mar 17; 11(3):958-68. doi: 10.1039/c4mb00649f. Epub 2015 Jan 22. PMID:  25609494

Bejugam P.R and Singh Shailza*(2016) Computing molecular devices in L.major through transcriptome analysis: Structured Simulation Approach. Plos One. DOI: 10.1371/journal.pone.0148909

Mandlik V, Shinde S, Singh Shailza*. (2014) Molecular evolution of the enzymes involved in the sphingolipid metabolism of Leishmania: selection pressure in relation to functional divergence and conservation. BMC Evol Biol. 2014 Jun 21; 14(1):142. [Epub ahead of print] PMID:  24951280 [PubMed - as supplied by publisher]

Shinde S, Mol M, Jamdar V, Singh Shailza*. (2014) Molecular modeling and molecular dynamics simulations of GPI 14 in Leishmania major: Insight into the catalytic site for active site directed drug design. J Theor Biol. 2014 Feb 25; 351C:37-46. doi: 10.1016/j.jtbi.2014.02.017. [Epub ahead of print] PMID: 24583312 [PubMed - as supplied by publisher]

Shinde S, Mol M, Singh Shailza*. (2014) Regulatory networks, genes and glycerophospholipid biosynthesis pathway in schistosomiasis: a systems biology view for pharmacological intervention.  Gene 2014 Oct 25; 550(2):214-22. doi: 10.1016/j.gene.2014.08.031. Epub 2014 Aug 19. PMID: 25149020 [PubMed - in process] 

Mol M, Patole MS, Singh Shailza*. (2014) Immune signal transduction in leishmaniasis from natural to artificial systems: role of feedback loop insertion. Biochim Biophys Acta. 2014 Jan; 1840(1):71-9. doi: 10.1016/j.bbagen.2013.08.018. Epub 2013 Aug 30. PMID: 23994140 [PubMed - indexed for MEDLINE]

*Corresponding author    

 

List of patents granted

(a) Number of Indian patents–with details on each patent

1. “A NOVEL CHIMERIC PROTEIN KINASE C AS AN IMMUNOMODULATOR” Indian Patent Application No. 201821005856

1) The chimeric protein kinase C is a novel designed protein constructed through synthetic device to act against infections caused by Leishmania.

2) The chimeric PKC of the present invention is capable of immune modulation via activation of NFkB signal transduction pathway in infected macrophages.

 

(b) Number of international patents–with brief details on each patent

PCT filed for “A novel chimeric protein kinase C as an immunomodulator” PCT/IN2019/050115

 

Book

Systems Biology Application in Synthetic Biology (Edited Volume) Springer Publishers DOI: 10.1007/978-81-322-2809-7

Synthetic Biology: Omics Tools and their Applications (Edited Volume with Springer Nature Publishers)

Systems and Synthetic Immunology (Edited Volume with Springer Nature Publishers) ISBN 978-981-15-3349-5

Metagenomic Systems Biology (Edited), Springer Nature ISBN:978-981-15-8562-3 (2020)

 

Book Chapters

 

Kabra R, Soni B, Kumar A, Chauhan N, Ingale P, Singh S* (2018). Integrated Systems and Chemical Biology Approach for Targeted Therapies. In Synthetic Biology 2018 (pp. 1-19). Springer Nature Singapore.

Milsee Mol, Vineetha Mandlik and Shailza Singh* (2016) Microbial Chassis assisting Retrosynthesis in book titled “Systems Biology application in Synthetic Biology”, Springer Publishers   DOI: 10.1007/978-81-322-2809-7.

Vineetha Mandlik, Pruthvi Raj Bejugam and Shailza Singh* (2014) “Application of ANN in Drug Discovery” in book titled “Artificial Neural Network for Drug Design, Delivery and Disposition”, Elsevier Inc.

Milsee Mol and Shailza Singh* (2013) "In silico Approaches for dealing with Gene Regulatory Network to understand the Molecular Mechanisms of Immunity in Infectious Disease" in Post Genomics Approaches in Drug Discovery, River Publishers.

Milsee Mol and Shailza Singh* (2013) "Computational Design of Biological Systems: From Systems to Synthetic Biology" in "Frontiers in Computational Chemistry", Bentham Science Publishers

Vineetha, Mandlik, Milsee, Mol., Sonali, Shinde and Shailza Singh* (2013). Gene Regulatory Network: A New Paradigm in Bioinformatics. Biotechnology, 6, Studium Press LLC, USA.

Sonali Shinde, Vineetha Mandlik and Shailza Singh* (2012) Chapter on Integrating Bioinformatics and Systems Biology for exploring novel lipid pathways in infectious Diseases for Bentham Science Publisher E-book titled “Advances in mathematical chemistry”

Shailza Singh* and Shinde, S. (2012) Chapter 16- Stochastic Simulation for Biochemical Reaction Networks in Infectious Disease. Medicinal Chemistry and Drug Design ISBN 978-953-51-0513-8. DOI: 10.5772/38245

*Corresponding author    

 

Reviews

Misra P, Singh S* (2019) Site Specific Microbiome of Leishmania Parasite and its Cross-talk with Immune Milieu. Immunol Lett. 2019 Oct 30. pii: S0165-2478(19)30388-8. doi: 10.1016/j.imlet.2019.10.004. [Epub ahead of print] Review. PMID: 31678358

Soni, B and Singh S* (2019) Cytokine Milieu in Infectious Disease: A Sword or a Boon. Journal of Interferon and Cytokine Research. 2019 Sep 24. doi: 10.1089/jir.2019.0089. [Epub ahead of print] PMID: 31553263

Misra P, Singh S*. (2019) Role of cytokines in combinatorial immunotherapeutics of non-small cell lung cancer through systems perspective. Cancer Med. 2019 Apr 17. doi: 10.1002/cam4.2112. [Epub ahead of print] PMID: 30997737 

Kabra R, Chauhan N, Kumar A, Ingale P, Singh S*. (2019) Efflux pumps and antimicrobial resistance: Paradoxical components in systems genomics. Prog Biophys Mol Biol. 2019 Jan; 141:15-24. doi: 10.1016/j.pbiomolbio.2018.07.008. Epub 2018 Jul 18. PMID: 30031023

Mol M, Raj Bejugam P, Singh S. (2014) Synthetic biology at the interface of functional genomics. Brief Funct Genomics. 2015 May;14(3):180-8. doi: 10.1093/bfgp/elu031. Epub 2014 Sep 10. PMID: 25212484

Mol M, Kabra R, Singh S*. (2018) Genome modularity and synthetic biology: Engineering systems. Prog Biophys Mol Biol. 2018 Jan; 132:43-51. doi: 10.1016/j.pbiomolbio.2017.08.002. Epub 2017 Aug 8. Review. PMID: 28801037

Soni B, Nimsarkar P, Mol M, Saha B, Singh S * (2018) Systems-synthetic biology in understanding the complexities and simple devices in immunology. Cytokine 108, pp60-66.

Mandlik V, Kabra R, Singh S*. (2017) System pharmacogenomics application in infectious diseases. Brief Funct Genomics. 2017 Mar 21. doi: 10.1093/bfgp/elx002. [Epub ahead of print] PMID: 28369182

*Corresponding author    

Professional recognition, awards, fellowships

  • Member of Board of Studies in Bioinformatics at D.Y. Patil University, Pune 2013-2017
  • Serving as Chancellor’s Nominee at Dr. B.R. Ambedkar Marathwada University, Aurangabad since 2017.
  • Rapid Grant for Young Investigator 2012
  • Selected by INSA for Bilateral Exchange Programme in "Chemometrics and Drug Delivery" 2012
  • Nominated by DBT for SAKURA EXCHANGE PROGRAMME IN SCIENCE, TOKYO 2018
  • DBT and CSIR Travel Award
  • Life Member-Indian Biophysical Society
  • Life Member -Biotechnology Society of India
  • Life Member-Society of Biological Chemists, India
  • Life Member-Association of Microbiologists of India (AMI)
  • Life Member-Association for DNA Fingerprinting and Diagnostics
  • Life Member-Proteomics Society of India (PSI)
  • Life Member-Indian Immunology Society (IIS)
  • Molecular Immunology Forum-nominated

Seminars

  • Invited talk on “Systems pharmacology strategies and discovery avenues in Bioactive Natural Products: (Re)-defining Lessons from the Past and Future” at GITAM University, Department of Biochemistry and Bioinformatics, Vizag, 26th-27th March 2015. 
  • Invited Talk on "Engineering signal transduction pathways through synthetic modular systems: Dissecting the puzzle in infectious disease" at 50th Indian Biophysical Society Conference, Jamia Millia Islamia, New Delhi, 14th-17th Feb 2015.
  • Key Note Talk on "Systems engineering and the integration of mechanistic explanation in infectious disease through synthetic biology::A golden braid" at Pre-Science Congress, Aurangabad, 30th-31st December 2014
  • Invited Talk on "Elucidating the interactome in Leishmania: Molecular insights with ligand pharmacophoric sites through combinatorial QSAR and Molecular Dynamics simulation" in a State-level Seminar titled "Recent Advances in Computational Medicinal Chemistry" on 14th November 2014 at Smt.Kashibai Navale College of Pharmacy, Singhad Technical Education Society, SP University of Pune, Pune.
  • Invited Talk on "Rational Drug Design in the Bioinformatics Era: Navigating the translational challenges through an integrated approach" in the Bioinformatics Workshop, ACTREC, Navi Mumbai, Kharghar, 23rd-24th April 2015.
  • Invited Talk onComputational System Biology and Synthetic Biology : The Future of Infectious Disease” at Jamia Millia Islamia, 14th October 2015, Hall No.202, S Ramanujan Block, Mujeeb Bagh, JMI, New Delhi
  • Invited Talk on “Systems and Synthetic Biology Approaches in Infectious Disease: Two sides of the same coin dealing with Validation and Variability” at TERI, New Delhi, 13th October 2015.
  • Invited Talk on “Paradoxical components in Biological circuit and negative autoregulation of transcriptional factors: A systems theoretic model in Leishmaniasis” at 14th FAOBMB Congress and 84th Annual Meeting of SBC (I), Hyderabad, 27th-30th November 2015.
  • Invited Talk on “Anti-leishmanial activity of coumarin derivatives: Network based drug design using mechanistic systems biology” at IIT Guwahati, Bioinformatics and Computer aided drug design conference, 7th December 2015.
  • Invited Talk on "Structure based design of a new series of coumarins as anti-leishmanial inhibitors" at Department of Biochemistry, MGIMS, Wardha, 9th-10th March 2017.
  • Invited talk on "Bioinformatics - Tool for Drug development of Natural products" at Garware College, 23rd March 2016, Pune.
  • Invited Talk on “Structureomics of the sphingolipid metabolism of the parasite Leishmania", National Symposium on Omics to Structural Basis of Diseases, 30th September-1st October 2016, MSU Vadodara, Gujarat.
  • Invited Lecture in DST Inspire Camp, Dayanand Science College, Latur, "Cells governing the Life in Science" (Four Lectures), 26th-27th September 2016.
  • Invited talk on "Dissecting and Optimizing Druggability through Network Modeling and Liposomal formulations" at National Seminar on Drug Development and Diagnostic Approaches for Tuberculosis Infection, July 29-30, 2016, Bhanuben Nanawati College of Pharmacy, Vile Parle, Mumbai.
  • Invited Talk on “Deciphering lipid metabolism in Leishmaniasis using systems perspective" Lipid Meet 2016, Amity University, Gurgaon, 14th-15th Dec 2016.
  • Invited talk on " Synthetic Bioengineering for Neglected Tropical Disease: A Computational Pipeline" at Interdisciplinary Biotechnology Unit, AMU, Aligarh, 16th-17th March 2017.
  • Invited talk on “Systems framework for Synthetic biology inspired therapy in Leishmaniasis” at Cross-Talk in Omics 2017, Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, August 9, 2017.
  • Plenary lecture  on “Signaling framework for Synthetic circuit immuno-modulation in Leishmaniasis: A Structural Perspective for Drug Delivery Systems at SBCADD 2018, Alagappa University, Karaikudi, 20th-23rd February 2018.

Teaching work such as:

Courses taught   :  Computer Application and Bioinformatics

Practicals conducted: Computer Application and Bioinformatics

Collaborations

1. Dr. Kanaujia, IIT Guwahati
2. Dr. Basu, IISER Pune


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