Derek J. Smith
Research Scientist
Singapore
Summary
With 24+ years of postgraduate and industry experience, a seasoned Research Scientist specializing in computational chemistry and structural bioinformatics. Expert in utilizing analytical and problem-solving skills to drive scientific advancements and improve productivity. Possesses extensive proficiency in various scientific and productivity software, resulting in accurate and efficient results. Demonstrates leadership, management, and team-working skills through interdisciplinary industrial projects and commitments to academic and voluntary work.
Overview
16
16
years of professional experience
13
13
years of post-secondary education
Work History
Research Scientist
Singapore Institute for Food and Biotechnology Innovation (SIFBI), A*STAR
11.2015 - 1 2024
- I was most recently employed at the Singapore Institute for Food and Biotechnology Innovation (SIFBI), a recently formed entity in A*STAR focusing on the use of biocatalytic routes towards flavours and fragrances. I have been working on several projects, including:
- Enzyme Engineering of a β-Cryptoxanthin Biosynthetic Pathway. A novel P450 from Euglena gracilis, which, among a family of dioxygenases, can only act as a monooxygenase. Sequence analysis and molecular modelling of this enzyme suggest that a novel N-terminal sequence is responsible for the monooxygenase activity.
- Biosynthesis of Irones. Irones are fragrant molecules found in the rhizomes of the iris plant and are of commercial interest. I identified an enzyme which has very low activity as an irone synthase. Using molecular modelling of the substrate conformation required for a-irone synthesis, we optimized the active site towards irone production through site-saturation mutagenesis and recombination.
- Biosynthesis of Filbertone. Filbertone is the main flavour molecule of the hazelnut (Corylus avellana), and very little is known about its biosynthesis. I have been using genome mining, along with sequence analysis and molecular modelling, to elucidate most of its biosynthetic pathway (manuscript in preparation).
- Biosynthetic Pathway Design. Industry partners to SIFBI occasionally suggest collaborations for biosynthetic routes to molecules of commercial interest. I have been involved with pathway design for such molecules, helping to identify enzymes of interest, and necessary optimization via protein engineering.
Senior Research Scientist
Bioinformatics Institute, A*STAR
11.2012 - 11.2015
- Employed under the IMaGIN (Industrial Microbiology and Genome Informatics) grant, supporting the Institute for Chemical and Engineering Sciences (ICES) Biomass-to-Chemicals program (2012-2015):
- A Biosynthetic Route to Acrylic Acid (with Dr. Farid Ghadessy (A*STAR p53 Laboratory)). I modeled the enzyme Lactoyl-CoA Dehydratase and its activator protein as part of an evolution project towards increasing the enzyme activity for acrylic acid production. I also designed a novel dehydratase-activator fusion protein, which demonstrated some activity.
- A Biosynthetic Route to Adipic Acid (with Dr. Liu Zhibin (ICES)). I modeled cytochrome P450 enzymes (CYP52A15, CYP153A, CYP102A3) and designed libraries to introduce activity towards hexanoic acid.
- I also worked with Dr. Ang Ee Lui (Metabolic Engineering Research Laboratory (MERL)) is looking to introduce substrate promiscuity into a fluorinase enzyme from Streptomyces cattleya. As a side project to this, I collaborated with Dr. Bob Robinson's lab (A*STAR IMCB) to solve the structure of a novel cyanobacterial chlorinase.
Staff Scientist (II)
Codexis Laboratories Singapore Pte Ltd
09.2008 - 09.2012
- Analysis of protein sequence and structural data in order to engineer novel activity into enzymes towards target substrates, as well as reaction optimization under industrially relevant process conditions.
- Collaborated with colleagues on various projects, sharing knowledge and expertise while working together towards common objectives.
- During the final year of CLS operations, I became the Acting Manager for the Molecular and Cellular Biology Group during a management interregnum.
Senior Post-Doctoral Fellow
Bioinformatics Institute, A*STAR
01.2005 - 09.2008
- As a post-doctoral fellow at the Bioinformatics Institute, my work focused on the modeling of kinases, in particular Protein Kinase-C (PKC) isoforms, and the EGFR/HER family of Receptor Tyrosine Kinases. I also modeled small molecule inhibitors into the enzyme active sites to understand the basis of selectivity and activity. I also modeled several other proteins and protein-substrate complexes (p53 homologues, Hydroxycinnamoyl-Coenzyme Hydratase Lyase, 6-oxo-Camphor Hydrolase). I used molecular dynamics software to model their behavior and identify activity changes due to mutations.
- Authored professional scientific papers for publishing in peer-reviewed journals.
- Contributed to research activities by providing specialist input based on professional expertise, practice, experience, and qualifications.
Post-Doctoral Research/Teaching Fellow
University of York, UK
01.2000 - 07.2004
- At the York Structural Biology Laboratory (YSBL) at the University of York, my focus was on the study and model refinement of antifreeze proteins through continued collaboration with Unilever Research, which involved both molecular modelling and some lab-based work, as well as modelling of proteins involved in the b-lactam biosynthetic pathway (Collaboration with ACS Dobfar, UK) and assisting fellow researchers with molecular modelling studies to enhance their protein structure research programs.
- Teaching responsibilities associated with my postgraduate and post-doctoral work have included the planning and execution of various computational courses for undergraduates and postgraduates, as well as Structural Bioinformatics courses for external academic and industrial professional participants. This involved lecturing and various assessments associated with these courses.
- Admissions Tutor in 2003 for the MRes in Bioinformatics, a one-year Masters course jointly taught by the Departments of Biology, Chemistry, and Computer Science.
Education
DPhil. - Chemistry
University of York, UK
09.1995 - 06.1999
BSc. (Hons) - Chemistry (2i)
University of York, UK
09.1992 - 06.1995
GCSE/A-Level - undefined
The Plume School, Maldon, Essex, UK
09.1985 - 06.1992
Skills
Bioinformatics
Computational Chemistry
Genome Mining
Biosynthetic Pathway Discovery
Enzyme Engineering
Directed Evolution
Research methods
Results interpretation
Experiment Design
Paper writing
Data Analytics
Research program planning
Project Support
Awards
Co-awarded (with a project team from Codexis) the 2012 Presidential Green Chemistry Challenge Award for “An Efficient Biocatalytic Process to Manufacture Simvastatin” by the U.S. Environmental Protection Agency (EPA).
References
Dr. Chandra Verma (Head of Biomolecular Modelling and Design Group)
Bioinformatics Institute,
30 Biopolis Street,
#07-01, Matrix,
Singapore 138671
Tel: +65-64788273
Email: chandra@bii.a-star.edu.sg
Dr. Ang Ee Lui (Department Leader, Strain Engineering)
Singapore Institute for Food and Biotechnology Innovation,
31 Biopolis Way,
#02-04, Nanos,
Singapore 138669
Tel: +65-62792725
Email: ang_ee_lui@sifbi.a-star.edu.sg
Dr. Steve Collier (Executive Director, Process & Analytical Development)
Sage Therapeutics, Inc.,
215 First Street,
Cambridge, MA 02142,
USA
Tel: +1-617-949-4303
Email: steven.collier@sagerx.com
Languages
English
Advanced (C1)
Software
MS/Linux/MacOS
Unix, Python
BLAST, CLUSTALO, HMMER
PyMOL, DS, MOE
MODELLER, AlphaFold
AUTODOCK Vina
MS Office
Timeline
Research Scientist
Singapore Institute for Food and Biotechnology Innovation (SIFBI), A*STAR
11.2015 - 1 2024
Senior Research Scientist
Bioinformatics Institute, A*STAR
11.2012 - 11.2015
Staff Scientist (II)
Codexis Laboratories Singapore Pte Ltd
09.2008 - 09.2012
Senior Post-Doctoral Fellow
Bioinformatics Institute, A*STAR
01.2005 - 09.2008
Post-Doctoral Research/Teaching Fellow
University of York, UK
01.2000 - 07.2004
DPhil. - Chemistry
University of York, UK
09.1995 - 06.1999
BSc. (Hons) - Chemistry (2i)
University of York, UK
09.1992 - 06.1995
GCSE/A-Level - undefined
The Plume School, Maldon, Essex, UK
09.1985 - 06.1992
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