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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] [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.
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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.
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Miryala SK, Basu S, Naha A, Debroy R, Ramaiah S, Anbarasu A, Natarajan S. Datasets comprising the quality validations of simulated protein-ligand complexes and SYBYL docking scores of bioactive natural compounds as inhibitors of Mycobacterium tuberculosis protein-targets. Data Brief 2022; 42:108146. [PMID: 35479419 PMCID: PMC9035630 DOI: 10.1016/j.dib.2022.108146] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/29/2022] [Accepted: 04/04/2022] [Indexed: 01/04/2023] Open
Abstract
Docking scores and simulation parameters to study the potency of natural compounds against protein targets in Mycobacterium tuberculosis (Mtb) were retrieved through molecular docking and in-silico structural investigation. The molecular docking datasets comprised 15 natural compounds, seven conventional anti-tuberculosis (anti-TB) drugs and their seven corresponding Mtb target proteins. Mtb protein targets were actively involved in translation mechanism, nucleic acid metabolism and membrane integrity. Standard structural screening and stereochemical optimizations were adopted to generate the 3D protein structures and their corresponding ligands prior to molecular docking. Force-field integration and energy minimization were further employed to obtain the proteins in their ideal geometry. Surflex-dock algorithm using Hammerhead scoring functions were used to finally produce the docking scores between each protein and the corresponding ligand(s). The best-docked complexes selected for simulation studies were subjected to topology adjustments, charge neutralizations, solvation and equilibrations (temperature, volume and pressure). The protein-ligand complexes and molecular dynamics parameter files have been provided. The trajectories of the simulated parameters such as density, pressure and temperature were generated with integrated tools of the simulation suite. The datasets can be useful to computational and molecular medicine researchers to find therapeutic leads relevant to the chemical behaviours of a specific class of compounds against biological systems. Structural parameters and energy functions provided a set of standard values that can be utilised to design simulation experiments regarding similar macromolecular interactions.
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Duan C, Jiang Q, Jiang X, Zeng H, Wu Q, Yu Y, Yang X. Discovery of a Novel Inhibitor Structure of Mycobacterium tuberculosis Isocitrate Lyase. Molecules 2022; 27:molecules27082447. [PMID: 35458645 PMCID: PMC9026967 DOI: 10.3390/molecules27082447] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis remains a global threat to public health, and dormant Mycobacterium tuberculosis leads to long-term medication that is harmful to the human body. M. tuberculosis isocitrate lyase (MtICL), which is absent in host cells, is a key rate-limiting enzyme of the glyoxylic acid cycle and is essential for the survival of dormant M. tuberculosis. The aim of this study was to evaluate natural compounds as potential MtICL inhibitors through docking and experimental verification. Screening of the TCMSP database library was done using Discovery Studio 2019 for molecular docking and interaction analysis, with the putative inhibitors of MtICL, 3-BP, and IA as reference ligands. Daphnetin (MOL005118), with a docking score of 94.8 and -CDOCKER interaction energy of 56 kcal/mol, was selected and verified on MtICL in vitro and M. smegmatis; daphnetin gave an IC50 of 4.34 μg/mL for the MtICL enzyme and an MIC value of 128 μg/mL against M. smegmatis, showing enhanced potential in comparison with 3-BP and IA. The interactions and essential amino acid residues of the protein were analyzed. In summary, natural daphnetin may be a promising new skeleton for the design of inhibitors of MtICL to combat dormant M. tuberculosis.
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Affiliation(s)
- Changyuan Duan
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, No. 1, Yixueyuan Road, Yuzhong Dist, Chongqing 400016, China; (C.D.); (X.J.); (H.Z.); (Q.W.); (Y.Y.)
| | - Qihua Jiang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China;
| | - Xue Jiang
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, No. 1, Yixueyuan Road, Yuzhong Dist, Chongqing 400016, China; (C.D.); (X.J.); (H.Z.); (Q.W.); (Y.Y.)
| | - Hongwei Zeng
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, No. 1, Yixueyuan Road, Yuzhong Dist, Chongqing 400016, China; (C.D.); (X.J.); (H.Z.); (Q.W.); (Y.Y.)
| | - Qiaomin Wu
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, No. 1, Yixueyuan Road, Yuzhong Dist, Chongqing 400016, China; (C.D.); (X.J.); (H.Z.); (Q.W.); (Y.Y.)
| | - Yang Yu
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, No. 1, Yixueyuan Road, Yuzhong Dist, Chongqing 400016, China; (C.D.); (X.J.); (H.Z.); (Q.W.); (Y.Y.)
| | - Xiaolan Yang
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, No. 1, Yixueyuan Road, Yuzhong Dist, Chongqing 400016, China; (C.D.); (X.J.); (H.Z.); (Q.W.); (Y.Y.)
- Correspondence: ; Tel.: +86-23-6848-5240
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Miryala SK, Basu S, Naha A, Debroy R, Ramaiah S, Anbarasu A, Natarajan S. Identification of bioactive natural compounds as efficient inhibitors against Mycobacterium tuberculosis protein-targets: A molecular docking and molecular dynamics simulation study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117340] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Kwon S, Chun HL, Ha HJ, Lee SY, Park HH. Heterogeneous multimeric structure of isocitrate lyase in complex with succinate and itaconate provides novel insights into its inhibitory mechanism. PLoS One 2021; 16:e0251067. [PMID: 33951112 PMCID: PMC8099091 DOI: 10.1371/journal.pone.0251067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/20/2021] [Indexed: 11/18/2022] Open
Abstract
During the glyoxylate cycle, isocitrate lyases (ICLs) catalyze the lysis of isocitrate to glyoxylate and succinate. Itaconate has been reported to inhibit an ICL from Mycobacterium tuberculosis (tbICL). To elucidate the molecular mechanism of ICL inhibition, we determined the crystal structure of tbICL in complex with itaconate. Unexpectedly, succinate and itaconate were found to bind to the respective active sites in the dimeric form of tbICL. Our structure revealed the active site architecture as an open form, although the substrate and inhibitor were bound to the active sites. Our findings provide novel insights into the conformation of tbICL upon its binding to a substrate or inhibitor, along with molecular details of the inhibitory mechanism of itaconate.
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Affiliation(s)
- Sunghark Kwon
- Department of Biotechnology, Konkuk University, Chungju, Chungbuk, Republic of Korea
| | - Hye Lin Chun
- College of Pharmacy, Chung-Ang University, Dongjak-gu, Seoul, Republic of Korea
| | - Hyun Ji Ha
- College of Pharmacy, Chung-Ang University, Dongjak-gu, Seoul, Republic of Korea
| | - So Yeon Lee
- College of Pharmacy, Chung-Ang University, Dongjak-gu, Seoul, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Dongjak-gu, Seoul, Republic of Korea
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