Samuel K E Gan

Agency of Science and Technology, Singapore, Bioinformatics, Faculty Member

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Papers by Samuel K E Gan

Essentially leading antibody production: An investigation of amino acids, myeloma and natural V-region signal peptides in producing Pertuzumab and Trastuzumab variants

Boosting the production of recombinant therapeutic antibodies is crucial in both academic and ind... more Boosting the production of recombinant therapeutic antibodies is crucial in both academic and industry settings. In this work, we investigated the usage of varying signal peptides by antibody genes and their roles in recombinant transient production. Comparing myeloma and the native signal peptides of both heavy and light chains in 168 antibody permutation variants, we performed a systematic analysis, finding amino acids counts to be involved in antibody production to construct a model for predicting co-transfection transient recombinant antibody production rates using the HEK293 system. The findings also provide insights into the usage of the large repertoire of antibody signal peptides.

An Alternative HIV-1 Non-Nucleoside Reverse Transcriptase Inhibition Mechanism: Targeting the p51 Subunit

Molecules

The ongoing development of drug resistance in HIV continues to push for the need of alternative d... more The ongoing development of drug resistance in HIV continues to push for the need of alternative drug targets in inhibiting HIV. One such target is the Reverse transcriptase (RT) enzyme which is unique and critical in the viral life cycle—a rational target that is likely to have less off-target effects in humans. Serendipitously, we found two chemical scaffolds from the National Cancer Institute (NCI) Diversity Set V that inhibited HIV-1 RT catalytic activity. Computational structural analyses and subsequent experimental testing demonstrated that one of the two chemical scaffolds binds to a novel location in the HIV-1 RT p51 subunit, interacting with residue Y183, which has no known association with previously reported drug resistance. This finding supports the possibility of a novel druggable site on p51 for a new class of non-nucleoside RT inhibitors that may inhibit HIV-1 RT allosterically. Although inhibitory activity was shown experimentally to only be in the micromolar range, t...

format_quoteTwo identified chemical scaffolds exhibited HIV-1 RT inhibition, suggesting non-canonical targeting mechanisms.format_quote

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Spontaneous Mutations in HIV-1 Gag, Protease, RT p66 in the First Replication Cycle and How They Appear: Insights from an In Vitro Assay on Mutation Rates and Types

International Journal of Molecular Sciences

While drug resistant mutations in HIV-1 are largely credited to its error prone HIV-1 RT, the tim... more While drug resistant mutations in HIV-1 are largely credited to its error prone HIV-1 RT, the time point in the infection cycle that these mutations can arise and if they appear spontaneously without selection pressures both remained enigmatic. Many HIV-1 RT mutational in vitro studies utilized reporter genes (LacZ) as a template to investigate these questions, thereby not accounting for the possible contribution of viral codon usage. To address this gap, we investigated HIV-1 RT mutation rates and biases on its own Gag, protease, and RT p66 genes in an in vitro selection pressure free system. We found rare clinical mutations with a general avoidance of crucial functional sites in the background mutations rates for Gag, protease, and RT p66 at 4.71 × 10−5, 6.03 × 10−5, and 7.09 × 10−5 mutations/bp, respectively. Gag and p66 genes showed a large number of ‘A to G’ mutations. Comparisons with silently mutated p66 sequences showed an increase in mutation rates (1.88 × 10−4 mutations/bp...

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The Determination of HIV-1 RT Mutation Rate, Its Possible Allosteric Effects, and Its Implications on Drug Resistance

The high mutation rate of human immunodeficiency virus type 1 (HIV-1) plays a major role in treat... more The high mutation rate of human immunodeficiency virus type 1 (HIV-1) plays a major role in treatment resistance from the development of vaccines to long-lasting drugs. In addressing the crux of the issue, various attempts to estimate the mutation rate of HIV-1 resulted in a large range of 10-5 - 10-3 errors/bp/cycle due to the use of different types of investigation methods. In this review, we discuss the different assay methods, their findings on the mutation rates of HIV-1 and how the location of these mutations can be further analyzed for their potential allosteric effects to reveal potentially new inhibitors with different pharmacodynamics that can be used to circumvent fast occurring HIV drug resistance. Given that HIV is one of the fastest mutating viruses, it is a good model for comprehensive study of its mutations that can give rise to much horizontal understanding towards overall viral drug resistance as well as emerging viral diseases.

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Reviewing HIV-1 Gag Mutations in Protease Inhibitors Resistance: Insights for Possible Novel Gag Inhibitor Designs

HIV treatment strategies against viral enzymes are continuously hampered by viral drug resistance... more HIV treatment strategies against viral enzymes are continuously hampered by viral drug resistance. Recent findings show that viral substrate Gag contributes to HIV-1 Protease Inhibitor (PI) resistance, leading to demands for new strategies in HIV treatment where Gag is recognized as a drug target. To successfully target Gag, there is a need of in-depth understanding of the Gag polyprotein and the effects of Gag mutations. Here, we propose new strategies in designing novel Gag inhibitors against existing and novel emerging Gag mutations via a structural understanding of the Gag-Protease relationship in PI resistance. In this review, we discuss the role of both novel and previously reported mutations, revealing insights to how they aid in PI resistance, and how new Gag inhibitors can be designed.

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Role of IgE-VH in FcεRIα and superantigen binding in allergy and immunotherapy

Journal of Allergy and Clinical Immunology

Modeling the full length HIV-1 Gag polyprotein reveals the role of its p6 subunit in viral maturation and the effect of non-cleavage site mutations in protease drug resistance

Journal of biomolecular structure & dynamics, Jan 27, 2017

HIV polyprotein Gag is increasingly found to contribute to protease inhibitor resistance. Despite... more HIV polyprotein Gag is increasingly found to contribute to protease inhibitor resistance. Despite its role in viral maturation and in developing drug resistance, there remain gaps in the knowledge of the role of certain Gag subunits (e.g. p6), and that of non-cleavage mutations in drug resistance. As p6 is flexible, it poses a problem for structural experiments, and is hence often omitted in experimental Gag structural studies. Nonetheless, as p6 is an indispensable component for viral assembly and maturation, we have modeled the full length Gag structure based on several experimentally determined constraints and studied its structural dynamics. Our findings suggest that p6 can mechanistically modulate Gag conformations. In addition, the full length Gag model reveals that allosteric communication between the non-cleavage site mutations and the first Gag cleavage site could possibly result in protease drug resistance, particularly in the absence of mutations in Gag cleavage sites. Ou...

Thyroid-SPOT for mobile devices: personalised thyroid treatment management app

Scientific Phone Apps and Mobile Devices

Thyroid-SPOT is a mobile application that allows users to be able to analyse thyroid function tes... more Thyroid-SPOT is a mobile application that allows users to be able to analyse thyroid function tests laboratory reports by computing the homeostatic euthyroid set point based on regressing thyroid function data according to a patented algorithm to define the parameters that maximize the goodness-of-fit to a negative exponential model for targetcentric individualized treatment. The app facilitates analysis and optimization of treatment plans, while also allowing both patients and doctors to stay up to date with a function that allows ".txt" files to be imported and exported to and from Dropbox. The app improves treatment monitoring, allowing clinical analysis to be on-the go, thus boosting healthcare.

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Cloning of Antibody Genes Using Unique Restrictions Sites

Use of Smartphone Apps for Biomedical Research

The Adaptor Protein BLNK Is Required for B Cell Antigen Receptor-induced Activation of Nuclear Factor-kappa B and Cell Cycle Entry and Survival of B Lymphocytes

Journal of Biological Chemistry, 2001

B lymphocytes lacking the adaptor protein B cell linker (BLNK) do not proliferate in response to ... more B lymphocytes lacking the adaptor protein B cell linker (BLNK) do not proliferate in response to B cell antigen receptor (BCR) engagement. We demonstrate here that BCR-activated BLNK ؊/؊ B cells fail to enter the cell cycle, and this is due to their inability to induce the expression of the cell cycle regulatory proteins such as cyclin D2 and cyclin-dependent kinase 4. BCR-stimulated BLNK ؊/؊ B cells also do not up-regulate the cell survival protein Bcl-x L , which may be necessary for the cells to complete the cell cycle. In addition, BLNK ؊/؊ B cells exhibit a high rate of spontaneous apoptosis in culture. Examination of the various BCR-activated signaling pathways in mouse BLNK ؊/؊ B cells reveals the intact activation of Akt and mitogen-activated protein kinases but the impaired activation of nuclear factor (NF)-B that is known to regulate genes involved in cell proliferation and survival. The inability to activate NF-B in BCR-stimulated BLNK ؊/؊ B cells is due to a failure to induce the degradation of the inhibitory B protein. In all these aspects, BLNK ؊/؊ B cells resemble xid B cells that have a mutation in Bruton's tyrosine kinase (Btk). Recently, phospholipase C (PLC)-␥2 has also been demonstrated to be essential for NF-B activation. Since BLNK has been shown separately to interact with both Btk and PLC-␥2, our finding of normal Btk but impaired PLC-␥2 activation in BCR-stimulated BLNK ؊/؊ B cells strongly suggests that BLNK orchestrates the formation of a Btk-PLC-␥2 signaling axis that regulates NF-B activation. Taken together, the NF-B activation defect may be sufficient to explain the similar defects in BCR-induced B cell proliferation and T cellindependent immune responses in BLNK ؊/؊ , Btk ؊/؊ , and PLC-␥2 ؊/؊ mice.

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Su.67. Establishing a Model for Examination of HER-2 Specific IgG and IgE Mediated Tumour Cell Killing

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Editorial: “Set My Scientists Free” - Scientific Phone Apps and DIY equipment during lockdowns.

Scientific Phone Apps and Mobile Devices, 2020

The SARS-CoV2 pandemic of year 2020 caused unprecedented disruptions globally. With lockdowns imp... more The SARS-CoV2 pandemic of year 2020 caused unprecedented disruptions globally. With lockdowns implemented in many countries, scientific research such as biomedical sciences, experienced major disruptions in the access and supply of research materials and equipment.
With these disruptions, the dependence of research on centralized infrastructure had become apparent. Without the scientific equipment and the associated infrastructure, many aspects of research grinded to a halt. Yet, this highlights the need for adaptations to build our own devices, particularly how scientific apps and mobile devices including the “Internet of Things” can help. In this, a phrase that I previously used to describe the early work of scientific phone apps – “Set My Scientists Free” seems apt to describe a much-needed change.

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Editorial: The promises of Microcontroller kits and Smartphone apps for Psychological research

Scientific Phone Apps and Mobile Devices, 2020

Traditional psychological research relying on the fixed location laboratories and surveys are fra... more Traditional psychological research relying on the fixed location laboratories and surveys are fraught with limitations. To an extent, these limits contribute to the serious problem of both poor reproducibility and poor ecological validity by constraining the geographical sampling of participant, affecting convenience and willingness. While this has been alleviated with the Internet revolution bringing along on-line surveys, the more recent Smartphone and microcontroller kit revolutions promise to break down the limitations even further. Drawing from examples of these revolutions in related disciplines, microcontroller kit revolutions can improve convenience and administration of psychological research, both survey-based and experimental.

format_quoteOnly 36% of studies from three journals were reproducible, highlighting significant irreproducibility in psychological research.format_quote

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