1
|
Song BPC, Ch'ng ACW, Lim TS. Review of phage display: A jack-of-all-trades and master of most biomolecule display. Int J Biol Macromol 2024; 256:128455. [PMID: 38013083 DOI: 10.1016/j.ijbiomac.2023.128455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
Phage display was first described by George P. Smith when it was shown that virus particles were capable of presenting foreign proteins on their surface. The technology has paved the way for the evolution of various biomolecules presentation and diverse selection strategies. This unique feature has been applied as a versatile platform for numerous applications in drug discovery, protein engineering, diagnostics, and vaccine development. Over the decades, the limits of biomolecules displayed on phage particles have expanded from peptides to proteomes and even alternative scaffolds. This has allowed phage display to be viewed as a versatile display platform to accommodate various biomolecules ranging from small peptides to larger proteomes which has significantly impacted advancements in the biomedical industry. This review will explore the vast array of biomolecules that have been successfully employed in phage display technology in biomedical research.
Collapse
Affiliation(s)
- Brenda Pei Chui Song
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
| |
Collapse
|
2
|
Song BPC, Lai JY, Lim TS. Generation of a Naïve Human scFv Phage Display Library and Panning Selection. Methods Mol Biol 2024; 2793:21-40. [PMID: 38526721 DOI: 10.1007/978-1-0716-3798-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Phage display antibody libraries have been successfully used as the essential tool to produce monoclonal antibodies against a plethora of targets ranging from diseases to native biologically important proteins as well as small molecules. It is well documented that diverse antibody genes are the major genetic source for the construction of a high-quality antibody library and selection of high-affinity antibodies. Naïve antibody libraries are derived using the IgM repertoire of healthy donors obtained from B-cells isolated from human peripheral blood mononuclear cell (PBMC). Single-chain fragment variable (scFv) is a routinely used format due to its smaller size and preference for phage display. The process involves the use of a two-step cloning method for library construction. The protocol also covers the biopanning process for target positive clone selection.
Collapse
Affiliation(s)
- Brenda Pei Chui Song
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang, Malaysia.
| |
Collapse
|
3
|
Lim TS, Kirupananther HP, Goodall S, King B. Stereotactic Cardiac Ablative Radiotherapy (SCAR) for Refractory Ventricular Tachycardia: Western Australia Experience. Int J Radiat Oncol Biol Phys 2023; 117:e191. [PMID: 37784827 DOI: 10.1016/j.ijrobp.2023.06.1056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Ventricular tachycardia is a potentially life-threatening cardiac condition that is associated with significant morbidity and mortality. Despite advances in medical therapies, implantable cardioverter-defibrillator (ICD) and catheter ablative therapy (CAT), some patients continue to suffer recurrent VT. SCAR is a highly accurate, non-invasive, and novel ablative therapeutic option that has shown promising results in the treatment of refractory VT patients associated with structural heart disease. Early case series and subsequent prospective clinical trials have demonstrated SCAR to be well-tolerated with acceptable safety profiles and consistently decreased VT episodes in VT patients, who failed all conventional antiarrhythmic medications and CAT. The aim of the current study is to report the efficacy and safety/tolerability of SCAR in ICD-dependent patients with refractory VT in Western Australia, Australia. MATERIALS/METHODS Seven patients with recurrent refractory VT, deemed high risk or non-suitable for CAT, were referred to GenesisCare at Fiona Stanley Hospital, Western Australia for SCAR between July 2020 and November 2022. Target volume definition and delineation involved interdisciplinary teams by combining all available clinical, electrophysiological mapping and diagnostic/planning cardiac imaging data to generate radiotherapy plans. Patients were treated whilst awake, with a single dose of 25 Gy using VMAT technique on the Synergy Linac with stereotactic X-ray tool capability. Efficacy was assessed by counting the number of episodes of VT and ICD shocks after SCAR. Safety and tolerability were evaluated by treatment related toxicities during follow up. RESULTS Of the seven patients referred for SCAR, only five received SCAR as two patients died from their refractory VT before their radiotherapy. For the patients receiving SCAR with at least 6 months follow-up, overall reduction in VT episodes and ICD shocks was 95% and 85%, respectively. No significant treatment-related toxicities were documented during follow-up. Two patients had died. Neither of their deaths were directly attributed to their radiotherapy. One patient died after requesting to cease her antiarrhythmic medications and to have her ICD switched off 2 days after SCAR (against medical advice). The other patient died 431 days after SCAR from aspiration pneumonia after fracturing her cervical spine following a fall at home and was unrelated to her VT. CONCLUSION Our data reflects international experience in terms of treatment efficacy and safety profiles of SCAR for patients with refractory VT. SCAR is increasingly recognized as an alternative cardiac ablative option for ICD-dependent VT patients who failed all conventional antiarrhythmic treatments. Nonetheless, careful patient selection and longer-term follow-up are required to ensure the optimal treatment outcomes can be achieved in these patients.
Collapse
Affiliation(s)
- T S Lim
- GenesisCare, Fiona Stanley Hospital, Murdoch, Perth, Western Australia, Australia
| | - H P Kirupananther
- GenesisCare, Fiona Stanley Hospital, Murdoch, Perth, Western Australia, Australia
| | - S Goodall
- GenesisCare, Fiona Stanley Hospital, Murdoch, Perth, Western Australia, Australia
| | - B King
- Fiona Stanley Hospital, Murdoch, Perth, Western Australia, Australia
| |
Collapse
|
4
|
Ng CL, Lim TS, Choong YS. Application of Computational Techniques in Antibody Fc-Fused Molecule Design for Therapeutics. Mol Biotechnol 2023:10.1007/s12033-023-00885-x. [PMID: 37742298 DOI: 10.1007/s12033-023-00885-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 08/23/2023] [Indexed: 09/26/2023]
Abstract
Since the advent of hybridoma technology in the year 1975, it took a decade to witness the first approved monoclonal antibody Orthoclone OKT39 (muromonab-CD3) in the year 1986. Since then, continuous strides have been made to engineer antibodies for specific desired effects. The engineering efforts were not confined to only the variable domains of the antibody but also included the fragment crystallizable (Fc) region that influences the immune response and serum half-life. Engineering of the Fc fragment would have a profound effect on the therapeutic dose, antibody-dependent cell-mediated cytotoxicity as well as antibody-dependent cellular phagocytosis. The integration of computational techniques into antibody engineering designs has allowed for the generation of testable hypotheses and guided the rational antibody design framework prior to further experimental evaluations. In this article, we discuss the recent works in the Fc-fused molecule design that involves computational techniques. We also summarize the usefulness of in silico techniques to aid Fc-fused molecule design and analysis for the therapeutics application.
Collapse
Affiliation(s)
- Chong Lee Ng
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Minden, Penang, Malaysia.
| |
Collapse
|
5
|
Alassiri M, Lai JY, Ch'ng ACW, Choong YS, Alanazi A, Lim TS. Subtractive panning for the isolation of monoclonal PEPITEM peptide antibody by phage display. Sci Rep 2023; 13:13627. [PMID: 37604859 PMCID: PMC10442400 DOI: 10.1038/s41598-023-40630-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/14/2023] [Indexed: 08/23/2023] Open
Abstract
Antibody phage display is a key tool for the development of monoclonal antibodies against various targets. However, the development of anti-peptide antibodies is a challenging process due to the small size of peptides for binding. This makes anchoring of peptides a preferred approach for panning experiments. A common approach is by using streptavidin as the anchor protein to present biotinylated peptides for panning. Here, we propose the use of recombinant expression of the target peptide and an immunogenic protein as a fusion for panning. The peptide inhibitor of trans-endothelial migration (PEPITEM) peptide sequence was fused to the Mycobacterium tuberculosis (Mtb) α-crystalline (AC) as an anchor protein. The panning process was carried out by subtractive selection of the antibody library against the AC protein first, followed by binding to the library to PEPITEM fused AC (PEPI-AC). A unique monoclonal scFv antibodies with good specificity were identified. In conclusion, the use of an alternative anchor protein to present the peptide sequence coupled with subtractive panning allows for the identification of unique monoclonal antibodies against a peptide target.
Collapse
Affiliation(s)
- Mohammed Alassiri
- Department of Basic Sciences, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Kingdom of Saudi Arabia.
- King Abdullah International Medical Research Center (KAIMRC), Riyadh, Kingdom of Saudi Arabia.
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), Ministry of the National Guard - Health Affairs, Riyadh, Kingdom of Saudi Arabia.
| | - Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Asma Alanazi
- King Abdullah International Medical Research Center (KAIMRC), Riyadh, Kingdom of Saudi Arabia
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Kingdom of Saudi Arabia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia.
| |
Collapse
|
6
|
Lai JY, Corona A, Ng CL, Tramontano E, Choong YS, Lim TS. Naïve antibody library derived monoclonal antibody against VP35 of Ebola virus. Int J Biol Macromol 2023:125571. [PMID: 37379953 DOI: 10.1016/j.ijbiomac.2023.125571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/13/2023] [Accepted: 06/24/2023] [Indexed: 06/30/2023]
Abstract
Ebola virus is notorious for causing severe and even deadly haemorrhagic fever in infected humans and non-human primates. The high fatality rate of Ebola virus disease (EVD) has highlighted the need for effective diagnosis and treatment. Two monoclonal antibodies (mAbs) have been approved by USFDA for treatment of EVD. Virus surface glycoprotein is the common target for diagnostic and therapy including vaccines. Even so, VP35, a viral RNA polymerase cofactor and interferon inhibitor could be a potential target to curb EVD. The present work describes the isolation of three mAb clones from a phage-displayed human naïve scFv library against recombinant VP35. The clones showed binding against rVP35 in vitro and inhibition of VP35 in luciferase reporter gene assay. Structural modelling analysis was also carried out to identify the binding interactions involved in the antibody-antigen interaction model. This allows some insight into the "fitness" of the binding pocket between the paratope and target epitope which would be useful for the design of new mAbs through in silico means in the future. In conclusion, the information obtained from the 3 isolated mAbs could be potentially useful in the quest to improve VP35 targeting for therapeutic development in the future.
Collapse
Affiliation(s)
- Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Chong Lee Ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
| |
Collapse
|
7
|
Khim Chan S, Yi Lai J, Gan CY, Soon Lim T. A Semi-Rational Mutagenesis Approach For Improved Substrate Activity Of Microbial Transglutaminase. Food Chem 2023; 419:136070. [PMID: 37030209 DOI: 10.1016/j.foodchem.2023.136070] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/12/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
A higher specific activity of microbial transglutaminase (mTGase) is desirable for a broad range of applications ranging from food industry to biotechnology. Three-dimensional docking simulation of mTGase revealed that residues V65, W69, and Y75 were critical for substrate recognition. A semi-rational mutagenesis approach was applied to each residue to generate three separate mini mutant libraries. A high-throughput screening process identified five mutants that demonstrated improved specific activities than the wild type (WT) mTGase were isolated from the Y75 mini mutant library. Mutant Y75L showed approximately 60% increment in specific activity and improved substrate specificity. Conjugation of two heterologous single-chain fragment variable clones to generate a diabody with mutant Y75L was successfully performed and validated. This work demonstrates the successful application of semi-rational mutagenesis coupled with a high-throughput screening approach to identify mTGase mutants with improved specific activities and specificities which are beneficial for protein-protein conjugation.
Collapse
|
8
|
Abstract
Phage display has been applied successfully for the rapid isolation of monoclonal antibodies against various targets including infectious diseases, autoantigens, cancer markers, and even small molecules. The main component in any phage display experiment is the availability of an antibody library to carry out the selection process of target-specific antibodies through an iterative process termed as biopanning. To generate human antibody libraries, the antibody repertoire can be obtained from human peripheral blood mononuclear cell (PBMC) or directly from cell-sorted B-cell populations. The choice of antibody isotype is dictated by the nature of the library. Naïve libraries would utilize IgM repertoires, whereas the IgG repertoire is commonly used for immune libraries. Antibody genes are amplified through polymerase chain reaction (PCR) and paired in a combinatorial fashion to expand the diversity of the cloned library repertoire. The protocol here describes the use of a two-step cloning method that can be applied for the construction of either a naïve or immune human antibody library in Fab format followed by the subsequent panning.
Collapse
Affiliation(s)
- Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia.
| |
Collapse
|
9
|
Nur A, Schubert M, Lai JY, Hust M, Choong YS, Isa WYHW, Lim TS. Antibody Phage Display. Methods Mol Biol 2023; 2702:3-12. [PMID: 37679612 DOI: 10.1007/978-1-0716-3381-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
The application of antibodies has transcended across many areas of work but mainly as a research tool, for diagnostic and for therapeutic applications. Antibodies are immunoproteins from vertebrates that have the unique property of specifically binding foreign molecules and distinguish target antigens. This property allows antibodies to effectively protect the host from infections. Apart from the hybridoma technology using transgenic animals, antibody phage display is commonly considered the gold standard technique for the isolation of human monoclonal antibodies. The concept of antibody phage display surrounds the ability to display antibody fragments on the surface of M13 bacteriophage particles with the corresponding gene packaged within the particle. A repetitive in vitro affinity based selection process permits the enrichment of target specific binders. This process of recombinant human monoclonal antibody generation also enables additional engineering for various applications. This makes phage display an indispensable technique for antibody development and engineering activities.
Collapse
Affiliation(s)
- Alia Nur
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Maren Schubert
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Wan Yus Haniff Wan Isa
- School of Medical Sciences, Department of Medicine, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia.
- Analytical Biochemistry Research Center, Universiti Sains Malaysia, Penang, Malaysia.
| |
Collapse
|
10
|
Ch'ng ACW, Konthur Z, Lim TS. Magnetic Nanoparticle-Based Semi-automated Panning for High-Throughput Antibody Selection. Methods Mol Biol 2023; 2702:291-313. [PMID: 37679626 DOI: 10.1007/978-1-0716-3381-6_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Bio-panning is a common process involved in recombinant antibody selection against defined targets. The biopanning process aims to isolate specific antibodies against an antigen via affinity selection from a phage display library. In general, antigens are immobilized on solid surfaces such as polystyrene plastic, magnetic beads, and nitrocellulose. For high-throughput selection, semi-automated panning selection allows simultaneous panning against multiple target antigens adapting automated particle processing systems such as the KingFisher Flex. The system setup allows for minimal human intervention for pre- and post-panning steps such as antigen immobilization, phage rescue, and amplification. In addition, the platform is also adaptable to perform polyclonal and monoclonal ELISA for the evaluation process. This chapter will detail the protocols involved from the selection stage until the monoclonal ELISA evaluation with important notes attached at the end of this chapter for optimization and troubleshooting purposes.
Collapse
Affiliation(s)
- Angela Chiew Wen Ch'ng
- Institute for Reseach in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Zoltán Konthur
- Department of Analytical Chemistry, Reference Materials, Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
| | - Theam Soon Lim
- Institute for Reseach in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia.
| |
Collapse
|
11
|
Lim TS, Ch'ng ACW, Song BPC, Lai JY. Streptavidin-Coated Solid-Phase Extraction (SPE) Tips for Antibody Phage Display Biopanning. Methods Mol Biol 2023; 2702:275-290. [PMID: 37679625 DOI: 10.1007/978-1-0716-3381-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Phage display is a technique that allows the presentation of unique proteins on the surface of bacteriophages. The phage particles are usually screened via repetitive rounds of antigen-guided selection and phage amplification. The main advantage of this approach lies in the physical linkage between phenotype and genotype. This feature allows the isolation of single unique clones from a panning campaign consisting of a highly diverse population of clones. Due to the high-throughput nature of this technique, different approaches have been developed to assist phage display selections. One of which involves utilizing a streptavidin-coated solid-phase extraction (SPE) tip that is mounted to an electronically controlled motorized multichannel pipette. In this chapter, we will entail the procedures involved in the adaptation of a commercial SPE tip (MSIA™ streptavidin D.A.R.T's®) as the solid phase. This protocol is an updated version of a previous protocol with some minor refinements.
Collapse
Affiliation(s)
- Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia.
| | - Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Brenda Pei Chui Song
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| |
Collapse
|
12
|
Ch'ng ACW, Schepergerdes L, Choong YS, Hust M, Lim TS. Antimicrobial antibodies by phage display: Identification of antibody-based inhibitor against mycobacterium tuberculosis isocitrate lyase. Mol Immunol 2022; 150:47-57. [PMID: 35987135 DOI: 10.1016/j.molimm.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/23/2022] [Accepted: 08/09/2022] [Indexed: 10/15/2022]
Abstract
The increasing incidence reports of antibiotic resistance highlights the need for alternative approaches to deal with bacterial infections. This brought about the idea of utilizing monoclonal antibodies as an alternative antibacterial treatment. Majority of the studies are focused on developing antibodies to bacterial surface antigens, with little emphasis on antibodies that inhibit the growth mechanisms of a bacteria host. Isocitrate lyase (ICL) is an important enzyme for the growth and survival of Mycobacterium tuberculosis (MTB) during latent infection as a result of its involvement in the mycobacterial glyoxylate and methylisocitrate cycles. It is postulated that the inhibition of ICL can disrupt the life cycle of MTB. To this extent, we utilized antibody phage display to identify a single chain fragment variable (scFv) antibody against the recombinant ICL protein from MTB. The soluble a-ICL-C6 scFv clone exhibited good binding characteristics with high specificity against ICL. More importantly, the clone exhibited in vitro inhibitory effect with an enzymatic assay resulting in a decrease of ICL enzymatic activity. In silico analysis showed that the scFv-ICL interactions are driven by 23 hydrogen bonds and 13 salt bridges that might disrupt the formation of ICL subunits for the tertiary structure or the formation of active site β domain. However, further validation is necessary to confirm if the isolated clone is indeed a good inhibitor against ICL for application against MTB.
Collapse
Affiliation(s)
- Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Lena Schepergerdes
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, 38106 Braunschweig
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, 38106 Braunschweig
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
| |
Collapse
|
13
|
Lim TS, Choong YS. In silico design of ACE2 mutants for competitive binding of SARS-CoV-2 receptor binding domain with hACE2. Physical Sciences Reviews 2022. [DOI: 10.1515/psr-2021-0136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The receptor binding motif (RBM) within the S-protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been touted as one of the main targets for vaccine/therapeutic development due to its interaction with the human angiotensin II converting enzyme 2 (hACE2) to facilitate virus entry into the host cell. The mechanism of action is based on the disruption of binding between the RBM and the hACE2 to prevent virus uptake for replication. In this work, we applied in silico approaches to design specific competitive binders for SARS-CoV-2 S-protein receptor binding motif (RBM) by using hACE2 peptidase domain (PD) mutants. Online single point mutation servers were utilised to estimate the effect of PD mutation on the binding affinity with RBM. The PD mutants were then modelled and the binding free energy was calculated. Three PD variants were designed with an increased affinity and interaction with SARS-CoV-2-RBM. It is hope that these designs could serve as the initial work for vaccine/drug development and could eventually interfere the preliminary recognition between SARS-CoV-2 and the host cell.
Collapse
Affiliation(s)
- Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia , Penang , Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia , Penang , Malaysia
| |
Collapse
|
14
|
Lim TS, Hust M, Visai L. Editorial: Recent Advances in Recombinant Antibody Therapeutics and Diagnostics for Infectious Diseases. Front Public Health 2022; 10:876889. [PMID: 35359788 PMCID: PMC8963948 DOI: 10.3389/fpubh.2022.876889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 02/18/2022] [Indexed: 11/25/2022] Open
Affiliation(s)
- Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, George Town, Malaysia
| | - Michael Hust
- Technische Universitat Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Berlin, Germany
| | - Livia Visai
- Department of Molecular Medicine, Centre for Health Technologies (CHT), Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali, Unità Operativa di Pavia, University of Pavia, Pavia, Italy
- Medicina Clinica-Specialistica, Unità Operativa di Ricerca 5 Laboratorio di Nanotecnologie, Istituti Clinici Scientifici Maugeri, Istituto di Ricovero e Cura a Carattere Scientifico, Pavia, Italy
| |
Collapse
|
15
|
Ng HM, Leo C, Lim TS, Low S, Ooi B. Corrigendum to “Polishing monoclonal antibody using pH-responsive TiO2/polysulfone membrane in dual size-exclusion strategy” [Sep. Purif. Technol. 213 (2019) 359–356]. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2021.119581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
16
|
Ch'ng ACW, Lam P, Alassiri M, Lim TS. Application of phage display for T-cell receptor discovery. Biotechnol Adv 2021; 54:107870. [PMID: 34801662 DOI: 10.1016/j.biotechadv.2021.107870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/23/2021] [Accepted: 11/15/2021] [Indexed: 12/13/2022]
Abstract
The immune system is tasked to keep our body unharmed and healthy. In the immune system, B- and T-lymphocytes are the two main components working together to stop and eliminate invading threats like virus particles, bacteria, fungi and parasite from attacking our healthy cells. The function of antibodies is relatively more direct in target recognition as compared to T-cell receptors (TCR) which recognizes antigenic peptides being presented on the major histocompatibility complex (MHC). Although phage display has been widely applied for antibody presentation, this is the opposite in the case of TCR. The cell surface TCR is a relatively large and complex molecule, making presentation on phage surfaces challenging. Even so, recombinant versions and modifications have been introduced to allow the growing development of TCR in phage display. In addition, the increasing application of TCR for immunotherapy has made it an important binding motif to be developed by phage display. This review will emphasize on the application of phage display for TCR discovery as well as the engineering aspect of TCR for improved characteristics.
Collapse
Affiliation(s)
- Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Paula Lam
- CellVec Private Limited, 118518, Singapore; National University of Singapore, Department of Physiology, 117597, Singapore; Duke-NUS Graduate Medical School, Cancer and Stem Cells Biology Program, 169857, Singapore
| | - Mohammed Alassiri
- Department of Basic Sciences, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia; King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
| |
Collapse
|
17
|
Balachandra D, Rahumatullah A, Lim TS, Mustafa FH, Ahmad H, Anuar NS, Noordin R. A new antigen detection ELISA for the diagnosis of Strongyloides infection. Acta Trop 2021; 221:105986. [PMID: 34058161 DOI: 10.1016/j.actatropica.2021.105986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/20/2021] [Accepted: 05/24/2021] [Indexed: 01/29/2023]
Abstract
Serodiagnosis is an essential component of the laboratory diagnosis of Strongyloides infection and is usually performed using an indirect IgG antibody test. A direct antigen detection method can complement the IgG assay, particularly for detecting early infection and post-treatment follow-up. In the present study, a recombinant scFv monoclonal antibody against NIE recombinant protein (rMAb23) that we had previously produced was used to develop a Strongyloides antigen detection ELISA (SsAg-ELISA). The assay is based on detecting immune complexes of circulating NIE antigens bound to Strongyloides-specific IgG antibodies. The optimized ELISA parameters were 10 µg/mL of rMAb23 coated on microtitre plate wells, 2% skim milk as blocking reagent, 1:100 serum dilution, and 1:1000 goat anti-human IgG F(ab')2 conjugated to horseradish peroxidase. Four groups of serum samples were used, i.e., Strongyloides-positive serum samples categorized into Groups IA and IB; the former were from probable chronic infections and the latter from probable early/acute infections. Strongyloides-negative samples comprising Groups II (healthy samples) and III (other infections); the latter were from eleven different types of other parasitic infections. The receiver operating characteristic (ROC) curve showed an area under the curve (AUC) of 1.00, cut-off optical density (OD405) of 0.5002, and 100% diagnostic sensitivity and specificity. The results of the commercial IgG-ELISA and SsAg-ELISA from Group IA were found to be moderately correlated (r = 0.416; p < 0.05). Notably, ANOVA showed that the average ODs405 of Group 1B were significantly higher (p < 0.05) than Group 1A, indicating that the assay may be useful to differentiate early and chronic infection. In conclusion, the developed SsAg-ELISA showed good diagnostic potential, and it merits further evaluation.
Collapse
Affiliation(s)
- Dinesh Balachandra
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia (USM), 11800 Penang, Malaysia
| | - Anizah Rahumatullah
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia (USM), 11800 Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia (USM), 11800 Penang, Malaysia
| | | | - Hussain Ahmad
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia (USM), 11800 Penang, Malaysia; Department of Microbiology, Abdul Wali Khan University Mardan, KPK, Pakistan
| | - Nor Suhada Anuar
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia (USM), 11800 Penang, Malaysia
| | - Rahmah Noordin
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia (USM), 11800 Penang, Malaysia.
| |
Collapse
|
18
|
Yeoh SG, Sum JS, Lai JY, W Isa WYH, Lim TS. Potential of Phage Display Antibody Technology for Cardiovascular Disease Immunotherapy. J Cardiovasc Transl Res 2021; 15:360-380. [PMID: 34467463 DOI: 10.1007/s12265-021-10169-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/22/2021] [Indexed: 11/26/2022]
Abstract
Cardiovascular disease (CVD) is one of the leading causes of death worldwide. CVD includes coronary artery diseases such as angina, myocardial infarction, and stroke. "Lipid hypothesis" which is also known as the cholesterol hypothesis proposes the linkage of plasma cholesterol level with the risk of developing CVD. Conventional management involves the use of statins to reduce the serum cholesterol levels as means for CVD prevention or treatment. The regulation of serum cholesterol levels can potentially be regulated with biological interventions like monoclonal antibodies. Phage display is a powerful tool for the development of therapeutic antibodies with successes over the recent decade. Although mainly for oncology, the application of monoclonal antibodies as immunotherapeutic agents could potentially be expanded to CVD. This review focuses on the concept of phage display for antibody development and discusses the potential target antigens that could potentially be beneficial for serum cholesterol management.
Collapse
Affiliation(s)
- Soo Ghee Yeoh
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Jia Siang Sum
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - W Y Haniff W Isa
- School of Medical Sciences, Department of Medicine, Universiti Sains Malaysia, Kubang Kerian, 16150, Kelantan, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800, Penang, Malaysia.
| |
Collapse
|
19
|
Lim TS, Montague-Cardoso K. Glycans housed by a bacteriophage enable rapid identification of glycan recognition patterns. Commun Biol 2021; 4:976. [PMID: 34385576 PMCID: PMC8361188 DOI: 10.1038/s42003-021-02474-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Glycans are a major composition of the cell surface that interacts with the surrounding environment. The ability to carry out glycan-binding profile studies has been mainly done with glycan arrays. However, glycan arrays are not easily adaptable for cell surface and in vivo glycan recognition assays. The Liquid Glycan Array (LiGA) reported recently by Sojitra et al. is an alternative glycan recognition assay that employs DNA barcoding, bioorthogonal ligation and deep sequencing technology. In LiGA, barcoded M13 virions are used to present glycans to allow rapid identification of binding partners based on sequence identity. This physical link between the glycan to the DNA sequence fitted in the phage genome provides an ingenious approach to maneuver glycan binding profile studies in various conditions.
Collapse
Affiliation(s)
- Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Pulau Pinang, Malaysia.
| | | |
Collapse
|
20
|
Abstract
The introduction of nucleic acid amplification techniques has revolutionized the field of medical diagnostics in the last decade. The advent of PCR catalyzed the increasing application of DNA, not just for molecular cloning but also for molecular based diagnostics. Since the introduction of PCR, a deeper understanding of molecular mechanisms and enzymes involved in DNA/RNA replication has spurred the development of novel methods devoid of temperature cycling. Isothermal amplification methods have since been introduced utilizing different mechanisms, enzymes, and conditions. The ease with which isothermal amplification methods have allowed nucleic acid amplification to be carried out has had a profound impact on the way molecular diagnostics are being designed after the turn of the millennium. With all the advantages isothermal amplification brings, the issues or complications surrounding each method are heterogeneous making it difficult to identify the best approach for an end-user. This review pays special attention to the various isothermal amplification methods by classifying them based on the mechanistic characteristics which include reaction formats, amplification information, promoter, strand break, and refolding mechanisms. We would also compare the efficiencies and usefulness of each method while highlighting the potential applications and detection methods involved. This review will serve as an overall outlook on the journey and development of isothermal amplification methods as a whole.
Collapse
Affiliation(s)
- Jörn Glökler
- Department of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | - Jeunice Ida
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | - Marcus Frohme
- Department of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
| |
Collapse
|
21
|
Choong YS, Lim TS, Liu H, Jiang R, Cai Z, Ge Y. Potential Inhibition of COVID-19 RNA-dependent RNA Polymerase by Hepatitis C Virus Non-nucleoside Inhibitors: An In-silico Perspective. LETT DRUG DES DISCOV 2021. [DOI: 10.2174/1570180817999201104123750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a
novel member of the genus betacoronavirus in the Coronaviridae family. It has been identified as
the causative agent of coronavirus disease 2019 (COVID-19), spreading rapidly in Asia, America
and Europe. Like some other RNA viruses, RNA replication and transcription of SARS-CoV-2 rely
on its RNA-dependent RNA polymerase (RdRP), which is a therapeutic target of clinical
importance. Crystal structure of SARS-CoV-2 was solved recently (PDB ID 6M71) with some
missing residues.
Objective:
We used SARS-CoV-2 RdRP as a target protein to screen for possible chemical
molecules with potential anti-viral effects.
Methods:
Here we modelled the missing residues 896-905 via homology modelling and then
analysed the interactions of Hepatitis C virus allosteric non-nucleoside inhibitors (NNIs) in the
reported NNIs binding sites in SARS-CoV-2 RdRP.
Results:
We found that MK-3281, filibuvir, setrobuvir and dasabuvir might be able to inhibit
SARS-CoV-2 RdRP based on their binding affinities in the respective binding sites.
Conclusion:
Further in vitro and in vivo experimental research will be carried out to evaluate their
effectiveness in COVID-19 treatment in the near future.
Collapse
Affiliation(s)
- Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Hanyun Liu
- Department of Infectious Diseases, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Rubin Jiang
- College of Marine Life Science, Ocean University of China, Qingdao, China
| | - Zimu Cai
- College of Marine Life Science, Ocean University of China, Qingdao, China
| | - Yuan Ge
- College of Marine Life Science, Ocean University of China, Qingdao, China
| |
Collapse
|
22
|
Lim CC, Chan SK, Lim YY, Ishikawa Y, Choong YS, Nagaoka Y, Lim TS. Development and structural characterisation of human scFv targeting MDM2 spliced variant MDM2 15kDa. Mol Immunol 2021; 135:191-203. [PMID: 33930714 DOI: 10.1016/j.molimm.2021.04.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/09/2021] [Accepted: 04/18/2021] [Indexed: 01/10/2023]
Abstract
The murine double minute 2 (MDM2) protein is a major negative regulator of the tumour suppressor protein p53. Under normal conditions, MDM2 constantly binds to p53 transactivation domain and/or ubiquinates p53 via its role as E3 ubiquitin ligase to promote p53 degradation as well as nuclear export to maintain p53 levels in cells. Meanwhile, amplification of MDM2 and appearance of MDM2 spliced variants occur in many tumours and normal tissues making it a prognostic indicator for human cancers. The mutation or deletion of p53 protein in half of human cancers inactivates its tumour suppressor activity. However, cancers with wild type p53 have its function effectively inhibited through direct interaction with MDM2 oncoprotein. Here, we described the construction of a MDM2 spliced variant (rMDM215kDa) consisting of SWIB/MDM2 domain and its central region for antibody generation. Biopanning with a human naïve scFv library generated four scFv clones specific to rMDM215kDa. Additionally, the selected scFv clones were able to bind to the recombinant full length MDM2 (rMDM2-FL). Computational prediction showed that the selected scFv clones potentially bind to exon 7-8 of MDM2 while leaving the MDM2/SWIB domain free for p53 interaction. The developed antibodies exhibit good specificity can be further investigated for downstream biomedical and research applications.
Collapse
Affiliation(s)
- Chia Chiu Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Soo Khim Chan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Yee Ying Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Yuya Ishikawa
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-cho Suita, Osaka, 564-8680, Japan
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Yasuo Nagaoka
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-cho Suita, Osaka, 564-8680, Japan
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800, Penang, Malaysia.
| |
Collapse
|
23
|
Lai JY, Inoue N, Oo CW, Kawasaki H, Lim TS. One-step synthesis of M13 phage-based nanoparticles and their fluorescence properties. RSC Adv 2021; 11:1367-1375. [PMID: 35424103 PMCID: PMC8693608 DOI: 10.1039/d0ra02835e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 12/15/2020] [Indexed: 11/21/2022] Open
Abstract
Fluorescent carbon nanoparticles have been gaining more attention in recent years for their excellent fluorescence properties and simple synthesis routes. Different carbon sources have been reported for fluorescent carbon nanoparticle synthesis but the use of virus particles as a carbon source is scarce. Herein, we report the utilization of M13 bacteriophage particles as the carbon source to synthesize phage-based nanoparticles through facile, one-step microwave heating. M13 bacteriophage is a nanosized filamentous virus particle with a single-stranded DNA genome encapsulated by a large number of coat proteins. These amino acid rich building blocks provide a substantial amount of carbon source for the synthesis of fluorescent nanoparticles. The resulting nanoparticles from M13 bacteriophage showed good water solubility and exhibited bright blue luminescence. The selectivity and sensitivity of the phage-based nanoparticles towards Fe(iii) ions showed a quenching effect with a linear correlation and a detection limit of 8.0 μM. This process highlights the potential application of virus particles as a source for the synthesis of fluorescent carbon nanoparticles and the sensing application.
Collapse
Affiliation(s)
- Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia 11800 Penang Malaysia +60-4-653-4803 +60-4-653-4852
| | - Naoya Inoue
- Department of Chemistry and Materials Engineering, Faculty of Chemistry, Materials and Bioengineering, Kansai University 3-3-35 Yamate-cho Suita-shi Osaka 564-8680 Japan +60-6-6368-0979
| | - Chuan Wei Oo
- School of Chemical Sciences, Universiti Sains Malaysia 11800 Minden Penang Malaysia
| | - Hideya Kawasaki
- Department of Chemistry and Materials Engineering, Faculty of Chemistry, Materials and Bioengineering, Kansai University 3-3-35 Yamate-cho Suita-shi Osaka 564-8680 Japan +60-6-6368-0979
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia 11800 Penang Malaysia +60-4-653-4803 +60-4-653-4852
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia 11800 Penang Malaysia
| |
Collapse
|
24
|
Mohd Ali MR, Sum JS, Aminuddin Baki NN, Choong YS, Nor Amdan NA, Amran F, Lim TS. Development of monoclonal antibodies against recombinant LipL21 protein of pathogenic Leptospira through phage display technology. Int J Biol Macromol 2020; 168:289-300. [PMID: 33310091 DOI: 10.1016/j.ijbiomac.2020.12.062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/05/2020] [Accepted: 12/07/2020] [Indexed: 01/06/2023]
Abstract
Leptospirosis is a potentially fatal zoonosis that is caused by spirochete Leptospira. The signs and symptoms of leptospirosis are usually varied, allowing it to be mistaken for other causes of acute febrile syndromes. Thus, early diagnosis and identification of a specific agent in clinical samples is crucial for effective treatment. This study was aimed to develop specific monoclonal antibodies against LipL21 antigen for future use in leptospirosis rapid and accurate immunoassay. A recombinant LipL21 (rLipL21) antigen was optimized for expression and evaluated for immunogenicity. Then, a naïve phage antibody library was utilized to identify single chain fragment variable (scFv) clones against the rLipL21 antigen. A total of 47 clones were analysed through monoclonal phage ELISA. However, after taking into consideration the background OD405 values, only 4 clones were sent for sequencing to determine human germline sequences. The sequence analysis showed that all 4 clones are identical. The in silico analysis of scFv-lip-1 complex indicated that the charged residues of scFv CDRs are responsible for the recognition with rLipL21 epitopes. The generated monoclonal antibody against rLipL21 will be evaluated as a detection reagent for the diagnosis of human leptospirosis in a future study.
Collapse
Affiliation(s)
- Mohammad Ridhuan Mohd Ali
- Bacteriology Unit, Infectious Disease Research Center (IDRC), Institute for Medical Research (IMR), 40170 Setia Alam, Malaysia
| | - Jia Siang Sum
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Nurul Najian Aminuddin Baki
- Bacteriology Unit, Infectious Disease Research Center (IDRC), Institute for Medical Research (IMR), 40170 Setia Alam, Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Nur Asyura Nor Amdan
- Bacteriology Unit, Infectious Disease Research Center (IDRC), Institute for Medical Research (IMR), 40170 Setia Alam, Malaysia
| | - Fairuz Amran
- Bacteriology Unit, Infectious Disease Research Center (IDRC), Institute for Medical Research (IMR), 40170 Setia Alam, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
| |
Collapse
|
25
|
Rahumatullah A, Ahmad A, Noordin R, Lai JY, Baharudeen Z, Lim TS. Applicability of Brugia malayi immune antibody library for the isolation of a human recombinant monoclonal antibody to Echinococcus granulosus antigen B. Exp Parasitol 2020; 219:108029. [DOI: 10.1016/j.exppara.2020.108029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/03/2020] [Accepted: 10/16/2020] [Indexed: 12/18/2022]
|
26
|
Lai JY, Lim TS. Infectious disease antibodies for biomedical applications: A mini review of immune antibody phage library repertoire. Int J Biol Macromol 2020; 163:640-648. [PMID: 32650013 PMCID: PMC7340592 DOI: 10.1016/j.ijbiomac.2020.06.268] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/21/2020] [Accepted: 06/28/2020] [Indexed: 12/18/2022]
Abstract
Antibody phage display is regarded as a critical tool for the development of monoclonal antibodies for infectious diseases. The different classes of antibody libraries are classified based on the source of repertoire used to generate the libraries. Immune antibody libraries are generated from disease infected host or immunization against an infectious agent. Antibodies derived from immune libraries are distinct from those derived from naïve libraries as the host's in vivo immune mechanisms shape the antibody repertoire to yield high affinity antibodies. As the immune system is constantly evolving in accordance to the health state of an individual, immune libraries can offer more than just infection-specific antibodies but also antibodies derived from the memory B-cells much like naïve libraries. The combinatorial nature of the gene cloning process would give rise to a combination of natural and un-natural antibody gene pairings in the immune library. These factors have a profound impact on the coverage of immune antibody libraries to target both disease-specific and non-disease specific antigens. This review looks at the diverse nature of antibody responses for immune library generation and discusses the extended potential of a disease-specified immune library in the context of phage display.
Collapse
Affiliation(s)
- Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
| |
Collapse
|
27
|
Ida J, Kuzuya A, Choong YS, Lim TS. An intermolecular-split G-quadruplex DNAzyme sensor for dengue virus detection. RSC Adv 2020; 10:33040-33051. [PMID: 35515051 PMCID: PMC9056686 DOI: 10.1039/d0ra05439a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 08/23/2020] [Indexed: 01/12/2023] Open
Abstract
Nucleic acids have special ability to organize themselves into various non-canonical structures, including a four-stranded DNA structure termed G-quadruplex (G4) that has been utilized for diagnostic and therapeutic applications. Herein, we report the ability of G4 to distinguish dengue virus (DENV) based on its serotypes (DENV-1, DENV-2, DENV-3 and DENV-4) using a split G4-hemin DNAzyme configuration. In this system, two separate G-rich oligonucleotides are brought together upon target DNA strand hybridization to form a three-way junction architecture, allowing the formation of a G4 structure. The G4 formation in complexation with hemin can thus provide a signal readout by generating a DNAzyme that is able to catalyze H2O2-mediated oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS). This results in a change of color providing a sensing platform for the colorimetric detection of DENV. In our approach, betaine and dimethyl sulfoxide were utilized for better G4 generation by enhancing the target-probe hybridization. In addition to this serotype-specific assay, a multi-probe cocktail assay, which is an all-in-one assay was also examined for DENV detection. The system highlights the potential of split G-quadruplex configurations for the development of DNA-based detection and serotyping systems in the future.
Collapse
Affiliation(s)
- Jeunice Ida
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia 11800 Penang Malaysia +60-4-653-4803 +60-4-653-4852
| | - Akinori Kuzuya
- Department of Chemistry and Materials Engineering, Kansai University 3-3-35 Yamate, Suita Osaka 564-8680 Japan
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia 11800 Penang Malaysia +60-4-653-4803 +60-4-653-4852
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia 11800 Penang Malaysia +60-4-653-4803 +60-4-653-4852
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia 11800 Penang Malaysia
| |
Collapse
|
28
|
Rahumatullah A, Lim TS, Yunus MH, Noordin R. Development of an Antigen Detection ELISA for Bancroftian Filariasis Using BmSXP-Specific Recombinant Monoclonal Antibody. Am J Trop Med Hyg 2020; 101:436-440. [PMID: 31162018 DOI: 10.4269/ajtmh.19-0034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Lymphatic filariasis is a mosquito-borne parasitic disease responsible for morbidity and disability that affects 1.2 billion people worldwide, mainly the poor communities. Currently, filarial antigen testing is the method of choice for the detection of bancroftian filariasis, and to date, there are two commonly used tests. In the present study, a recently reported recombinant monoclonal antibody (5B) specific to BmSXP filarial antigen was used in developing an ELISA for the detection of circulating filarial antigen in sera of patients with bancroftian filariasis. The performance of the ELISA was evaluated using 124 serum samples. The ELISA was positive with all sera from microfilaremic bancroftian filariasis patients (n = 34). It also showed 100% diagnostic specificity when tested with sera from 50 healthy individuals and 40 patients with other parasitic diseases. The developed assay using the novel 5B recombinant monoclonal antibody could potentially be a promising alternative antigen detection test for bancroftian filariasis.
Collapse
Affiliation(s)
- Anizah Rahumatullah
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Muhammad Hafiznur Yunus
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Rahmah Noordin
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Pulau Pinang, Malaysia
| |
Collapse
|
29
|
Lim YY, Lim TS, Choong YS. Human IgG1 Fc pH-dependent optimization from a constant pH molecular dynamics simulation analysis. RSC Adv 2020; 10:13066-13075. [PMID: 35492131 PMCID: PMC9051383 DOI: 10.1039/c9ra10712f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/11/2020] [Indexed: 11/21/2022] Open
Abstract
The binding of IgG Fc with FcRn enables the long circulating half-life of IgG, where the Fc–FcRn complex interacts in a pH-dependent manner. This complex shows stronger interaction at pH ≤ 6.5 and weaker interaction at pH ≥ 7.4. The Fc–FcRn binding mechanism that promotes the long circulating half-life of IgG has prompted several IgG Fc-related mutational studies to focus on the pH-dependent Fc–FcRn complex interactions in order to improve the pharmacokinetic properties of Fc. Hence, in this study, we applied the in silico constant pH molecular dynamics (CpHMD) simulation approach to evaluate the human Fc–FcRn complex binding (pH 6.0) and dissociating (pH 7.5) mechanism at the molecular level. The analysis showed that the protonated state of the titratable residues changes from pH 6.0 to pH 7.5, where the disrupting energy for Fc–FcRn complex formation was found to be due to the electrostatic repulsion between the complex. According to the analysis, an Fc variant was computationally designed with an improved binding affinity at pH 6.0, which is still able to dissociate at pH 7.5 with FcRn at the in silico level. The binding free energy calculation via the MMPB/GBSA approach showed that the designed Fc mutant (MutM4) has increased binding affinity only at pH 6.0 compared with the reported mutant (YTE) Fc. This work demonstrates an alternative Fc design with better binding properties for FcRn, which can be useful for future experimental evaluation and validation. An in silico IgG-Fc variant with better affinity at pH 6.0 but retained the dissociation at pH 7.5 was designed.![]()
Collapse
Affiliation(s)
- Yee Ying Lim
- Institute for Research in Molecular Medicine (INFORMM)
- Universiti Sains Malaysia
- 11800 Minden
- Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine (INFORMM)
- Universiti Sains Malaysia
- 11800 Minden
- Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine (INFORMM)
- Universiti Sains Malaysia
- 11800 Minden
- Malaysia
| |
Collapse
|
30
|
Kamal NNSBNM, Lim TS, Ismail R, Choong YS. Conformations and interactions comparison between R- and S-methadone in wild type CYP2B6, 2D6 and 3A4. Physical Sciences Reviews 2019. [DOI: 10.1515/psr-2018-0172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Methadone is a morphine-substitute drug in methadone maintenance treatment (MMT) program to treat patients with opioid dependency. However, the methadone clinical effects are depending on the methadone metabolism rates that vary among the patients with genetic polymorphism of cytochrome P450s (CYPs). Our previous study showed methadone has different binding affinity due to the polymorphisms in CYP2B6, CYP2D6 and CYP3A4 that could contribute to the methadone metabolism rate. In this work, the conformation and interactions of R- and S-methadone in wild type CYP2B6, CYP2D6 and CYP3A4 were further studied in order to understand behaviour of R- and S-methadone at the CYP binding site. Clustering analysis showed that the conformation of R- and S-methadone in CYP2B6 are most stable, thus could lead to a higher efficiency of methadone metabolism. The conformation fluctuation of methadone in CYP2D6 could due to relatively smaller binding pocket compared with CYP2B6 and CYP3A4. The binding sites volumes of the studied CYPs were also found to be increased upon the binding with methadone. Therefore, this might contributed to the interactions of both R- and S-methadone in CYPs were mainly by hydrophobic contacts, van der Waals and electrostatic interactions. In the future, should an inhibitor for CYP is to be designed to prolong the prolonged opioid effect, the inhibitor should cater for single CYP isozyme as this study observed the behavioural differences of methadone in CYP isozymes.
Graphical Abstract:
Collapse
|
31
|
Lim CC, Woo PCY, Lim TS. Development of a Phage Display Panning Strategy Utilizing Crude Antigens: Isolation of MERS-CoV Nucleoprotein human antibodies. Sci Rep 2019; 9:6088. [PMID: 30988390 PMCID: PMC6465254 DOI: 10.1038/s41598-019-42628-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 04/04/2019] [Indexed: 12/20/2022] Open
Abstract
Antibody phage display has been pivotal in the quest to generate human monoclonal antibodies for biomedical and research applications. Target antigen preparation is a main bottleneck associated with the panning process. This includes production complexity, downstream purification, quality and yield. In many instances, purified antigens are preferred for panning but this may not be possible for certain difficult target antigens. Here, we describe an improved procedure of affinity selection against crude or non-purified antigen by saturation of non-binders with blocking agents to promote positive binder enrichment termed as Yin-Yang panning. A naïve human scFv library with kappa light chain repertoire with a library size of 109 was developed. The improved Yin-Yang biopanning process was able to enrich monoclonal antibodies specific to the MERS-CoV nucleoprotein. Three unique monoclonal antibodies were isolated in the process. The Yin-Yang biopanning method highlights the possibility of utilizing crude antigens for the isolation of monoclonal antibodies by phage display.
Collapse
Affiliation(s)
- Chia Chiu Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800, Penang, Malaysia.
| |
Collapse
|
32
|
Lim CC, Choong YS, Lim TS. Cognizance of Molecular Methods for the Generation of Mutagenic Phage Display Antibody Libraries for Affinity Maturation. Int J Mol Sci 2019; 20:E1861. [PMID: 30991723 PMCID: PMC6515083 DOI: 10.3390/ijms20081861] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 12/25/2022] Open
Abstract
Antibodies leverage on their unique architecture to bind with an array of antigens. The strength of interaction has a direct relation to the affinity of the antibodies towards the antigen. In vivo affinity maturation is performed through multiple rounds of somatic hypermutation and selection in the germinal centre. This unique process involves intricate sequence rearrangements at the gene level via molecular mechanisms. The emergence of in vitro display technologies, mainly phage display and recombinant DNA technology, has helped revolutionize the way antibody improvements are being carried out in the laboratory. The adaptation of molecular approaches in vitro to replicate the in vivo processes has allowed for improvements in the way recombinant antibodies are designed and tuned. Combinatorial libraries, consisting of a myriad of possible antibodies, are capable of replicating the diversity of the natural human antibody repertoire. The isolation of target-specific antibodies with specific affinity characteristics can also be accomplished through modification of stringent protocols. Despite the ability to screen and select for high-affinity binders, some 'fine tuning' may be required to enhance antibody binding in terms of its affinity. This review will provide a brief account of phage display technology used for antibody generation followed by a summary of different combinatorial library characteristics. The review will focus on available strategies, which include molecular approaches, next generation sequencing, and in silico approaches used for antibody affinity maturation in both therapeutic and diagnostic applications.
Collapse
Affiliation(s)
- Chia Chiu Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang 11800, Malaysia.
| |
Collapse
|
33
|
Ch'ng ACW, Chan SK, Ignatius J, Lim TS. Human T-cell receptor V gene segment of alpha and beta families: A revised primer design strategy. Eur J Immunol 2019; 49:1186-1199. [PMID: 30919413 DOI: 10.1002/eji.201747328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 02/28/2019] [Accepted: 03/25/2019] [Indexed: 11/11/2022]
Abstract
The application of human TCR in cancer immunotherapy has gained momentum with developments in tumor killing strategies using endogenous adaptive immune responses. The successful coverage of a diverse TCR repertoire is mainly attributed to the primer design of the human TCR V genes. Here, we present a refined primer design strategy of the human TCR V gene by clustering V gene sequence homolog for degenerate primer design based on the data from IMGT. The primers designed were analyzed and the PCR efficiency of each primer set was optimized. A total of 112 alpha and 160 beta sequences were aligned and clustered using a phylogram yielding 32 and 27 V gene primers for the alpha and beta family. The new primer set was able to provide 93.75% and 95.63% coverage for the alpha and beta family, respectively. A semi-qualitative approach using the designed primer set was able to provide a relative view of the TCR V gene diversity in different populations. Taken together, the new primers provide a more comprehensive coverage of the TCR gene diversity for improved TCR library generation and TCR V gene analysis studies.
Collapse
Affiliation(s)
- Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Soo Khim Chan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Joshua Ignatius
- Warwick Manufacturing Group, University of Warwick, Coventry, United Kingdom
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia.,Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang, Malaysia
| |
Collapse
|
34
|
Melvin Ng H, Leo C, Lim TS, Low S, Ooi B. Polishing monoclonal antibody using pH-responsive TiO2/polysulfone membrane in dual size-exclusion strategy. Sep Purif Technol 2019. [DOI: 10.1016/j.seppur.2018.12.053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
35
|
Ida J, Chan SK, Glökler J, Lim YY, Choong YS, Lim TS. G-Quadruplexes as An Alternative Recognition Element in Disease-Related Target Sensing. Molecules 2019; 24:E1079. [PMID: 30893817 PMCID: PMC6471233 DOI: 10.3390/molecules24061079] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/14/2019] [Accepted: 03/16/2019] [Indexed: 12/05/2022] Open
Abstract
G-quadruplexes are made up of guanine-rich RNA and DNA sequences capable of forming noncanonical nucleic acid secondary structures. The base-specific sterical configuration of G-quadruplexes allows the stacked G-tetrads to bind certain planar molecules like hemin (iron (III)-protoporphyrin IX) to regulate enzymatic-like functions such as peroxidase-mimicking activity, hence the use of the term DNAzyme/RNAzyme. This ability has been widely touted as a suitable substitute to conventional enzymatic reporter systems in diagnostics. This review will provide a brief overview of the G-quadruplex architecture as well as the many forms of reporter systems ranging from absorbance to luminescence readouts in various platforms. Furthermore, some challenges and improvements that have been introduced to improve the application of G-quadruplex in diagnostics will be highlighted. As the field of diagnostics has evolved to apply different detection systems, the need for alternative reporter systems such as G-quadruplexes is also paramount.
Collapse
Affiliation(s)
- Jeunice Ida
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Soo Khim Chan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Jörn Glökler
- Division of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany.
| | - Yee Ying Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang 11800, Malaysia.
| |
Collapse
|
36
|
Lee YV, Choi SB, Wahab HA, Lim TS, Choong YS. Applications of Ensemble Docking in Potential Inhibitor Screening for Mycobacterium tuberculosis Isocitrate Lyase Using a Local Plant Database. J Chem Inf Model 2019; 59:2487-2495. [PMID: 30840452 DOI: 10.1021/acs.jcim.8b00963] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Isocitrate lyase (ICL) is a persistent factor for the survival of dormant stage Mycobacterium tuberculosis (MTB), thus a potential drug target for tuberculosis treatment. In this work, ensemble docking approach was used to screen for potential inhibitors of ICL. The ensemble conformations of ICL active site were obtained from molecular dynamics simulation on three dimer form systems, namely the apo ICL, ICL in complex with metabolites (glyoxylate and succinate), and ICL in complex with substrate (isocitrate). Together with the ensemble conformations and the X-ray crystal structures, 22 structures were used for the screening against Malaysian Natural Compound Database (NADI). The top 10 compounds for each ensemble conformation were selected. The number of compounds was then further narrowed down to 22 compounds that were within the Lipinski's Rule of Five for drug-likeliness and were also docked into more than one ensemble conformation. Theses 22 compounds were furthered evaluate using whole cell assay. Some compounds were not commercially available; therefore, plant crude extracts were used for the whole cell assay. Compared to itaconate (the known inhibitor of ICL), crude extracts from Manilkara zapota, Morinda citrifolia, Vitex negundo, and Momordica charantia showed some inhibition activity. The MIC/MBC value were 12.5/25, 12.5/25, 0.78/1.6, and 0.39/1.6 mg/mL, respectively. This work could serve as a preliminary study in order to narrow the scope for high throughput screening in the future.
Collapse
Affiliation(s)
- Yie-Vern Lee
- Institute for Research in Molecular Medicine (INFORMM) , Universiti Sains Malaysia , 11800 Minden , Penang , Malaysia
| | - Sy Bing Choi
- School of Data Science , Perdana University , 43400 Sri Kembangan , Selangor , Malaysia
| | - Habibah A Wahab
- Pharmaceutical Design and Simulation Laboratory, School of Pharmaceutical Sciences , Universiti Sains Malaysia , 11800 Minden , Penang , Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine (INFORMM) , Universiti Sains Malaysia , 11800 Minden , Penang , Malaysia.,Analytical Biochemistry Research Centre , Universiti Sains Malaysia , 11800 Minden , Penang , Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine (INFORMM) , Universiti Sains Malaysia , 11800 Minden , Penang , Malaysia
| |
Collapse
|
37
|
Affiliation(s)
- Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Stephan Klatt
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang, Malaysia
| |
Collapse
|
38
|
Soong JX, Chan SK, Lim TS, Choong YS. Optimisation of human V H domain antibodies specific to Mycobacterium tuberculosis heat shock protein (HSP16.3). J Comput Aided Mol Des 2019; 33:375-385. [PMID: 30689080 DOI: 10.1007/s10822-019-00186-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/22/2019] [Indexed: 11/29/2022]
Abstract
Mycobacterium tuberculosis (Mtb) 16.3 kDa heat shock protein 16.3 (HSP16.3) is a latency-associated antigen that can be targeted for latent tuberculosis (TB) diagnostic and therapeutic development. We have previously developed human VH domain antibodies (dAbs; clone E3 and F1) specific against HSP16.3. In this work, we applied computational methods to optimise and design the antibodies in order to improve the binding affinity with HSP16.3. The VH domain antibodies were first docked to the dimer form of HSP16.3 and further sampled using molecular dynamics simulation. The calculated binding free energy of the HSP16.3-dAb complexes showed non-polar interactions were responsible for the antigen-antibody association. Per-residue free energy decomposition and computational alanine scanning have identified one hotspot residue for E3 (Y391) and 4 hotspot residues for F1 (M394, Y396, R397 and M398). These hotspot residues were then mutated and evaluated by binding free energy calculations. Phage ELISA assay was carried out on the potential mutants (E3Y391W, F1M394E, F1R397N and F1M398Y). The experimental assay showed improved binding affinities of E3Y391W and F1M394E against HSP16.3 compared with the wild type E3 and F1. This case study has thus showed in silico methods are able to assist in optimisation or improvement of antibody-antigen binding.
Collapse
Affiliation(s)
- Jia Xin Soong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Minden, 11800, Penang, Malaysia
| | - Soo Khim Chan
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Minden, 11800, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Minden, 11800, Penang, Malaysia.,Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Minden, 11800, Penang, Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Minden, 11800, Penang, Malaysia.
| |
Collapse
|
39
|
Chan SK, Kuzuya A, Choong YS, Lim TS. DNA Switch: Toehold-Mediated DNA Isothermal Amplification for Dengue Serotyping. SLAS DISCOVERY: Advancing the Science of Drug Discovery 2018; 24:68-76. [DOI: 10.1177/2472555218791743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The inherent ability of nucleic acids to recognize a complementary pair has gained wide popularity in DNA sensor applications. DNA molecules can be produced in bulk and easily incorporated with various nanomaterials for sensing applications. More complex designs and sophisticated DNA sensors have been reported over the years to allow DNA detection in a faster, cheaper, and more convenient manner. Here, we report a DNA sensor designed to function like a switch to turn “on” silver nanocluster (AgNC) generation in the presence of a specific DNA target. By defining the probe region sequence, we are able to tune the color of the AgNC generated in direct relation to the different targets. As a proof of concept, we used dengue RNA-dependent RNA polymerase conserved sequences from all four serotypes as targets. This method was able to distinguish each dengue serotype by generating the serotype-respective AgNCs. The DNA switch was also able to identify and amplify the correct target in a mixture of targets with good specificity. This strategy has a detection limit of between 1.5 and 2.0 µM depending on the sequence of AgNC. The DNA switch approach provides an attractive alternative for single-target or multiplex DNA detection.
Collapse
Affiliation(s)
- Soo Khim Chan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Akinori Kuzuya
- Department of Chemistry and Materials Engineering, Kansai University, Yamate, Suita, Osaka, Japan
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Minden, Penang, Malaysia
| |
Collapse
|
40
|
Abstract
The application of recombinant human antibodies is growing rapidly mainly in the field of diagnostics and therapeutics. To identify antibodies against a specific antigen, panning selection is carried out using different display technologies. Phage display technology remains the preferred platform due to its robustness and efficiency in biopanning experiments. There are both manual and semi-automated panning selections using polystyrene plastic, magnetic beads, and nitrocellulose as the immobilizing solid surface. Magnetic nanoparticles allow for improved antigen binding due to their large surface area. The Kingfisher Flex magnetic particle processing system was originally designed to aid in RNA, DNA, and protein extraction using magnetic beads. However, the system can be programmed for antibody phage display panning. The automation allows for a reduction in human error and improves reproducibility in between selections with the preprogrammed movements. The system requires minimum human intervention to operate; however, human intervention is needed for post-panning steps like phage rescue. In addition, polyclonal and monoclonal ELISA can be performed using the semi-automated platform to evaluate the selected antibody clones. This chapter will summarize the suggested protocol from the panning stage till the monoclonal ELISA evaluation. Other than this, important notes on the possible optimization and troubleshooting are also included at the end of this chapter.
Collapse
Affiliation(s)
- Angela Chiew Wen Ch'ng
- Analytical Biochemistry Research Centre, Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | - Nurul Hamizah Binti Hamidon
- Analytical Biochemistry Research Centre, Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | - Zoltán Konthur
- Max Planck Institute of Colloids and Interfaces, Mühlenberg 1, 14476, Potsdam, Germany
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia. .,Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Minden, Penang, Malaysia.
| |
Collapse
|
41
|
Abstract
This protocol describes the processes involved in the generation of human antibody libraries in Fab format. The antibody repertoire is derived from peripheral blood mononucleocytes focusing on different immunoglobulin isotypes. A two-step cloning process was used to generate a diverse human Fab library for subsequent selection by phage display. The method can be applied for the generation of both naive and immune antibody libraries. The naive repertoire allows for the library to be applied for the generation of human monoclonal antibodies against a broad range of target antigens making it a useful resource for antibody generation. However, the immune repertoire will be focused against target antigens from a particular disease. The protocol will focus on the generation of the library including the panning process.
Collapse
Affiliation(s)
- Noorsharmimi Omar
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia. .,Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Minden, Penang, Malaysia.
| |
Collapse
|
42
|
Ng WK, Lim TS, Lai NS. Human neonatal Fc receptor as a new potential antibody binding protein for antibody immobilization. Biotechnol Appl Biochem 2017; 65:547-553. [PMID: 29280199 DOI: 10.1002/bab.1636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 12/15/2017] [Indexed: 11/11/2022]
Abstract
A critical challenge in producing an antibody-based assay with the highest reproducibility and sensitivity is the strategy to immobilize antibodies to solid phase. To date, numerous methods of antibody immobilization were reported but each was subjected to its advantages and limitations. The current study proposes a new potential antibody binding protein, the human neonatal fragment crystallizable (Fc) receptor. This protein has shown its high affinity to the Fc of antibody either in vivo or in vitro. Human neonatal Fc receptor is a heterodimer constructed by p51 α-heavy chain and β2-microglobulin light chain; however, the binding sites toward the antibody are located in the p51 α-heavy chain. Hence, vector cloning and recombinant protein expression were carried out to express the p51 α-heavy chain of the human neonatal Fc receptor (hFcRn-α). The recombinant protein expressed, hFcRn-α, was adopted to pin rabbit IgG against hepatitis B virus surface antigen to a solid phase. A sandwich enzyme-linked immunosorbent assay was further developed to evaluate the efficiency of hFcRn-α-directed immobilization in antigen detection. The result was compared with the conventional physical adsorption method. The findings demonstrated that human neonatal Fc receptor was efficient in pinning antibodies and generating higher signals compared with the physical adsorption of antibody.
Collapse
Affiliation(s)
- Woei Kean Ng
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Ngit Shin Lai
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Pulau Pinang, Malaysia
| |
Collapse
|
43
|
Leong SW, Lim TS, Ismail A, Choong YS. Integration of molecular dynamics simulation and hotspot residues grafting for de novo scFv design against Salmonella Typhi TolC protein. J Mol Recognit 2017; 31:e2695. [PMID: 29230887 DOI: 10.1002/jmr.2695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/13/2017] [Accepted: 11/19/2017] [Indexed: 01/10/2023]
Abstract
With the development of de novo binders for protein targets from non-related scaffolds, many possibilities for therapeutics and diagnostics have been created. In this study, we described the use of de novo design approach to create single-chain fragment variable (scFv) for Salmonella enterica subspecies enterica serovar Typhi TolC protein. Typhoid fever is a global health concern in developing and underdeveloped countries. Rapid typhoid diagnostics will improve disease management and therapy. In this work, molecular dynamics simulation was first performed on a homology model of TolC protein in POPE membrane bilayer to obtain the central structure that was subsequently used as the target for scFv design. Potential hotspot residues capable of anchoring the binders to the target were identified by docking "disembodied" amino acid residues against TolC surface. Next, scFv scaffolds were selected from Protein Data Bank to harbor the computed hotspot residues. The hotspot residues were then incorporated into the scFv scaffold complementarity determining regions. The designs recapitulated binding energy, shape complementarity, and interface surface area of natural protein-antibody interfaces. This approach has yielded 5 designs with high binding affinity against TolC that may be beneficial for the future development of antigen-based detection agents for typhoid diagnostics.
Collapse
Affiliation(s)
- Siew Wen Leong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Asma Ismail
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan, Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Minden, Penang, Malaysia
| |
Collapse
|
44
|
Malini S, Goh BL, Lim TS. A Rare Case of Roseomonas gilardii Peritonitis in a Patient on Continuous Ambulatory Peritoneal Dialysis. Perit Dial Int 2017; 36:578. [PMID: 27659935 DOI: 10.3747/pdi.2016.00103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- S Malini
- Nephrology Department, Hospital Serdang, Selangor
| | - B L Goh
- Nephrology Department, Hospital Serdang, Selangor
| | - T S Lim
- Nephrology Unit, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Serdang, Malaysia
| |
Collapse
|
45
|
Omar N, Hamidon NH, Yunus MH, Noordin R, Choong YS, Lim TS. Generation and selection of naïve Fab library for parasitic antigen: Anti‐
Bm
SXP antibodies for lymphatic filariasis. Biotechnol Appl Biochem 2017; 65:346-354. [DOI: 10.1002/bab.1591] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 08/16/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Noorsharmimi Omar
- Institute for Research in Molecular MedicineUniversiti Sains Malaysia Minden Penang Malaysia
| | - Nurul Hamizah Hamidon
- Institute for Research in Molecular MedicineUniversiti Sains Malaysia Minden Penang Malaysia
| | - Muhammad Hafiznur Yunus
- Institute for Research in Molecular MedicineUniversiti Sains Malaysia Minden Penang Malaysia
| | - Rahmah Noordin
- Institute for Research in Molecular MedicineUniversiti Sains Malaysia Minden Penang Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular MedicineUniversiti Sains Malaysia Minden Penang Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular MedicineUniversiti Sains Malaysia Minden Penang Malaysia
- Analytical Biochemistry Research CentreUniversiti Sains Malaysia Penang Malaysia
| |
Collapse
|
46
|
Hamidon NH, Suraiya S, Sarmiento ME, Acosta A, Norazmi MN, Lim TS. Immune TB Antibody Phage Display Library as a Tool To Study B Cell Immunity in TB Infections. Appl Biochem Biotechnol 2017; 184:852-868. [DOI: 10.1007/s12010-017-2582-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/15/2017] [Indexed: 12/30/2022]
|
47
|
Soong JX, Lim TS, Choong YS. The structural insights of 16.3 kDa heat shock protein (HSP16.3) from Mycobacterium tuberculosis via in silico study. Molecular Simulation 2017. [DOI: 10.1080/08927022.2017.1346254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Jia Xin Soong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Minden, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Minden, Malaysia
- ADAPT Research Cluster, Centre for Research Initiatives – Clinical and Health Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Minden, Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Minden, Malaysia
- ADAPT Research Cluster, Centre for Research Initiatives – Clinical and Health Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| |
Collapse
|
48
|
Chin CF, Lai JY, Choong YS, Anthony AA, Ismail A, Lim TS. Delineation of B-cell Epitopes of Salmonella enterica serovar Typhi Hemolysin E: Potential antibody therapeutic target. Sci Rep 2017; 7:2176. [PMID: 28526816 PMCID: PMC5438399 DOI: 10.1038/s41598-017-01987-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 04/05/2017] [Indexed: 11/09/2022] Open
Abstract
Hemolysin E (HlyE) is an immunogenic novel pore-forming toxin involved in the pathogenesis of typhoid fever. Thus, mapping of B-cell epitopes of Salmonella enterica serovar Typhi (S. Typhi) is critical to identify key immunogenic regions of HlyE. A random 20-mer peptide library was used for biopanning with enriched anti-HlyE polyclonal antibodies from typhoid patient sera. Bioinformatic tools were used to refine, analyze and map the enriched peptide sequences against the protein to identify the epitopes. The analysis identified both linear and conformational epitopes on the HlyE protein. The predicted linear GAAAGIVAG and conformational epitope PYSQESVLSADSQNQK were further validated against the pooled sera. The identified epitopes were then used to isolate epitope specific monoclonal antibodies by antibody phage display. Monoclonal scFv antibodies were enriched for both linear and conformational epitopes. Molecular docking was performed to elucidate the antigen-antibody interaction of the monoclonal antibodies against the epitopes on the HlyE monomer and oligomer structure. An in-depth view of the mechanistic and positional characteristics of the antibodies and epitope for HlyE was successfully accomplished by a combination of phage display and bioinformatic analysis. The predicted function and structure of the antibodies highlights the possibility of utilizing the antibodies as neutralizing agents for typhoid fever.
Collapse
Affiliation(s)
- Chai Fung Chin
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Amy Amilda Anthony
- Institute for Research in Molecular Medicine, Health Campus, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Asma Ismail
- Institute for Research in Molecular Medicine, Health Campus, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800, Penang, Malaysia.
| |
Collapse
|
49
|
Fischbach J, Loh Q, Bier FF, Lim TS, Frohme M, Glökler J. Alizarin Red S for Online Pyrophosphate Detection Identified by a Rapid Screening Method. Sci Rep 2017; 7:45085. [PMID: 28338022 PMCID: PMC5364467 DOI: 10.1038/srep45085] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/20/2017] [Indexed: 12/29/2022] Open
Abstract
We identified Alizarin Red S and other well known fluorescent dyes useful for the online detection of pyrophosphate in enzymatic assays, including the loop mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR) assays. An iterative screening was used for a selected set of compounds to first secure enzyme compatibility, evaluate inorganic pyrophosphate sensitivity in the presence of manganese as quencher and optimize conditions for an online detection. Of the selected dyes, the inexpensive alizarin red S was found to selectively detect pyrophosphate under LAMP and PCR conditions and is superior with respect to its defined red-shifted spectrum, long shelf life and low toxicity. In addition, the newly identified properties may also be useful in other enzymatic assays which do not generate nucleic acids but are based on inorganic pyrophosphate. Finally, we propose that our screening method may provide a blueprint for rapid screening of compounds for detecting inorganic pyrophosphate.
Collapse
Affiliation(s)
- Jens Fischbach
- Division Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Qiuting Loh
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Frank F. Bier
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Marcus Frohme
- Division Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Jörn Glökler
- Division Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| |
Collapse
|
50
|
Abstract
The incident of two children in Europe who died of diphtheria due to a shortage of anti-toxin drugs has highlighted the need for alternative anti-toxins. Historically, antiserum produced from immunised horses have been used to treat diphtheria. Despite the potential of antiserum, the economical and medial concerns associated with the use of animal antiserum has led to its slow market demise. Over the years, new and emerging infectious diseases have grown to be a major global health threat. The emergence of drug-resistant superbugs has also pushed the boundaries of available therapeutics to deal with new infectious diseases. Antibodies have emerged as a possible alternative to combat the continuous onslaught of various infectious agents. The isolation of antibodies against pathogens of infectious diseases isolated from immune libraries utilising phage display has yielded promising results in terms of affinities and neutralizing activities. This chapter focuses on the concept of immune antibody libraries and highlights the application of immune antibody libraries to generate antibodies for various infectious diseases.
Collapse
Affiliation(s)
- Soo Khim Chan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Minden, 11800, Penang, Malaysia.
| |
Collapse
|