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.
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...
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...
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.
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.
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...
About Us • New Joint BII-p53 Lab. • Setup in late 2013. • Main research direction is on drug desi... more About Us • New Joint BII-p53 Lab. • Setup in late 2013. • Main research direction is on drug design and development. • In our collaborations and research, we have developed a few useful applications. • A Proof-of-Concept that we can dedicate part of our processes for applications of science without compromising on the research. • This talk will focus on 2 problem statements as evidence for our successes in application. Problem Statement 1 • Smartphones are increasingly popular. • High penetration brings great convenience. – Emails, Whatsapp/Line/Skype etc.. Internet browsers. • Lack of bioinformatics apps in this platform for research use. • Bioinformatics apps allow for increased productivity in research. • Demand higher for "enablers" rather than "convenient" apps. • Need "enablers" that allows for analysis of ab1 single-pass sequencing files.
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.
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.
The therapeutic potential of immunoglobulin M (IgM) is of considerable interest in immunotherapy ... more The therapeutic potential of immunoglobulin M (IgM) is of considerable interest in immunotherapy due to its complement-activating and cell-agglutinating abilities. Pertuzumab and Trastuzumab are monoclonal antibodies used to treat human epidermal growth factor receptor 2 (HER2)-positive breast cancer but exhibit significantly different binding affinities as IgM when compared to its IgG isotype. Using integrative multiscale modelling and simulations of complete antibody assemblies, we show that Pertuzumab IgM is able to utilize all of its V-regions to bind multiple HER2 receptors simultaneously, while similar binding in Trastuzumab IgM is prohibited by steric clashes caused by the large globular domain of HER2. This is subsequently validated by confirming that Pertuzumab IgM inhibits proliferation in HER2 over-expressing live cells more effectively than its IgG counterpart and Trastuzumab IgM. Our study highlights the importance of understanding the molecular details of antibody-antigen interactions for the design and isotype selection of therapeutic antibodies.
The high mutation rate of the human immunodeficiency virus type 1 (HIV-1) plays a major role in t... more The high mutation rate of the human immunodeficiency virus type 1 (HIV-1) plays a major role in treatment resistance, from the development of vaccines to therapeutic 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 locations of mutations can be further analyzed for their allosteric effects to allow for new inhibitor designs. Given that HIV is one of the fastest mutating viruses, it serves as a good model for the comprehensive study of viral mutations that can give rise to a more horizontal understanding towards overall viral drug resistance as well as emerging viral diseases.
In studying the topic of civility and its association to other parameters, we modified Forni's Tw... more In studying the topic of civility and its association to other parameters, we modified Forni's Twenty-Five Rules of Considerate Conduct into an inventory for assessing civility. 220 Singapore residents completed an online survey that included a demographic survey, the civility inventory, SCS-R, and REI-40. Self-reported civility was correlated with age (r (214) = .134, p = .049), and experientiality (r (210) = .255, p < .001), but inversely correlated with social anxiety (r (210) =-.172, p = .013). There were no gender effects for civility (p = .014, r = .11), self-consciousness dimensions, and experientiality, even though males scored significantly higher on rationality (p = .013, r = .17). No effects were found for indicators of SES on civility scores. Our findings suggest that social standing may not necessarily be the most important factor as often presumed.
With the multitude of academic reports published daily, ever-increasing reference formats and sty... more With the multitude of academic reports published daily, ever-increasing reference formats and styles, it has become cumbersome for academics and researchers to create references and read all relevant publications. To alleviate these problems, the “Antibody & Product Development Lab (APD) Reference App” was created for easy reference search, and citation in different formats by using Optical Character Recognition (OCR) to capture the Digital Object Identifier (DOI) or title of a publication. Following this, users can easily retrieve, browse, and read translated summaries of the articles of interest. Incorporating Natural Language Processing (NLP), the app is available on both Google and Apple app stores with trials available for paid features.
The humanization of antibodies for therapeutics is a critical process that can determine the succ... more The humanization of antibodies for therapeutics is a critical process that can determine the success of antibody drug development. However, the science underpinning this process remains elusive with different laboratories having very different methods. Well-funded laboratories can afford automated high-throughput screening methods to derive their best binder utilizing a very expensive initial set of equipment affordable only to a few. Often within these high-throughput processes, only standard key parameters, such as production, binding and aggregation are analyzed. Given the lack of suitable animal models, it is only at clinical trials that immunogenicity and allergy adverse effects are detected through anti-human antibodies as per FDA guidelines. While some occurrences that slip through can be mitigated by additional desensitization protocols, such adverse reactions to grafted humanized antibodies can be prevented at the humanization step. Considerations such as better antibody localization, avoidance of unspecific interactions to superantigens and the tailoring of antibody dependent triggering of immune responses, the antibody persistence on cells, can all be preemptively considered through a holistic sagacious approach, allowing for better outcomes in therapy and for research and diagnostic purposes. Statement of Significance: Recent investigations of antibody elements have revealed effects that when combined with already known functions of elements such as isotypes, can open a new frontier in antibody humanization to reduce adverse effects in sagacious design.
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.
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...
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...
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.
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.
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...
About Us • New Joint BII-p53 Lab. • Setup in late 2013. • Main research direction is on drug desi... more About Us • New Joint BII-p53 Lab. • Setup in late 2013. • Main research direction is on drug design and development. • In our collaborations and research, we have developed a few useful applications. • A Proof-of-Concept that we can dedicate part of our processes for applications of science without compromising on the research. • This talk will focus on 2 problem statements as evidence for our successes in application. Problem Statement 1 • Smartphones are increasingly popular. • High penetration brings great convenience. – Emails, Whatsapp/Line/Skype etc.. Internet browsers. • Lack of bioinformatics apps in this platform for research use. • Bioinformatics apps allow for increased productivity in research. • Demand higher for "enablers" rather than "convenient" apps. • Need "enablers" that allows for analysis of ab1 single-pass sequencing files.
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.
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.
The therapeutic potential of immunoglobulin M (IgM) is of considerable interest in immunotherapy ... more The therapeutic potential of immunoglobulin M (IgM) is of considerable interest in immunotherapy due to its complement-activating and cell-agglutinating abilities. Pertuzumab and Trastuzumab are monoclonal antibodies used to treat human epidermal growth factor receptor 2 (HER2)-positive breast cancer but exhibit significantly different binding affinities as IgM when compared to its IgG isotype. Using integrative multiscale modelling and simulations of complete antibody assemblies, we show that Pertuzumab IgM is able to utilize all of its V-regions to bind multiple HER2 receptors simultaneously, while similar binding in Trastuzumab IgM is prohibited by steric clashes caused by the large globular domain of HER2. This is subsequently validated by confirming that Pertuzumab IgM inhibits proliferation in HER2 over-expressing live cells more effectively than its IgG counterpart and Trastuzumab IgM. Our study highlights the importance of understanding the molecular details of antibody-antigen interactions for the design and isotype selection of therapeutic antibodies.
The high mutation rate of the human immunodeficiency virus type 1 (HIV-1) plays a major role in t... more The high mutation rate of the human immunodeficiency virus type 1 (HIV-1) plays a major role in treatment resistance, from the development of vaccines to therapeutic 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 locations of mutations can be further analyzed for their allosteric effects to allow for new inhibitor designs. Given that HIV is one of the fastest mutating viruses, it serves as a good model for the comprehensive study of viral mutations that can give rise to a more horizontal understanding towards overall viral drug resistance as well as emerging viral diseases.
In studying the topic of civility and its association to other parameters, we modified Forni's Tw... more In studying the topic of civility and its association to other parameters, we modified Forni's Twenty-Five Rules of Considerate Conduct into an inventory for assessing civility. 220 Singapore residents completed an online survey that included a demographic survey, the civility inventory, SCS-R, and REI-40. Self-reported civility was correlated with age (r (214) = .134, p = .049), and experientiality (r (210) = .255, p < .001), but inversely correlated with social anxiety (r (210) =-.172, p = .013). There were no gender effects for civility (p = .014, r = .11), self-consciousness dimensions, and experientiality, even though males scored significantly higher on rationality (p = .013, r = .17). No effects were found for indicators of SES on civility scores. Our findings suggest that social standing may not necessarily be the most important factor as often presumed.
With the multitude of academic reports published daily, ever-increasing reference formats and sty... more With the multitude of academic reports published daily, ever-increasing reference formats and styles, it has become cumbersome for academics and researchers to create references and read all relevant publications. To alleviate these problems, the “Antibody & Product Development Lab (APD) Reference App” was created for easy reference search, and citation in different formats by using Optical Character Recognition (OCR) to capture the Digital Object Identifier (DOI) or title of a publication. Following this, users can easily retrieve, browse, and read translated summaries of the articles of interest. Incorporating Natural Language Processing (NLP), the app is available on both Google and Apple app stores with trials available for paid features.
The humanization of antibodies for therapeutics is a critical process that can determine the succ... more The humanization of antibodies for therapeutics is a critical process that can determine the success of antibody drug development. However, the science underpinning this process remains elusive with different laboratories having very different methods. Well-funded laboratories can afford automated high-throughput screening methods to derive their best binder utilizing a very expensive initial set of equipment affordable only to a few. Often within these high-throughput processes, only standard key parameters, such as production, binding and aggregation are analyzed. Given the lack of suitable animal models, it is only at clinical trials that immunogenicity and allergy adverse effects are detected through anti-human antibodies as per FDA guidelines. While some occurrences that slip through can be mitigated by additional desensitization protocols, such adverse reactions to grafted humanized antibodies can be prevented at the humanization step. Considerations such as better antibody localization, avoidance of unspecific interactions to superantigens and the tailoring of antibody dependent triggering of immune responses, the antibody persistence on cells, can all be preemptively considered through a holistic sagacious approach, allowing for better outcomes in therapy and for research and diagnostic purposes. Statement of Significance: Recent investigations of antibody elements have revealed effects that when combined with already known functions of elements such as isotypes, can open a new frontier in antibody humanization to reduce adverse effects in sagacious design.
First Class Behaviours for First World Nations, 2014
The awareness of others can be defined simply as being in full knowledge of: 1) the different nee... more The awareness of others can be defined simply as being in full knowledge of: 1) the different needs; 2) the desires; 3) the presence of; 4) and the actions of others in our daily activities. These daily activities can include walking, driving, cycling, eating, swimming, and standing in public or any shared facilities. It is essential to have a gracious and productive society, and both good habits and behaviors are necessary for its continued maintenance. Some theories underlying many of these behaviors and why we need to address them are included. For those whose interest is roused, a more detailed background of these theories is included in the "Additional Reading" at the end of this chapter.
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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.
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.