TEMPERATURE EFFECTS ON THE STABILITY OF MYCOBACTERIUM TUBERCULO-SIS SHIKIMATE KINASE (MtSK): STRATEGIES FOR SECURE TRANSPORT

Main Article Content

Aji Wibowo
Tinta Komariyah
Erwahyuni Endang Prabandari
Titin Ariyani
Eka Siska

Abstract

Mycobacterium tuberculosis Shikimate Kinase (MtSK) has a crucial role in the shikimic pathway, which is essential for this bacteria but is absent in humans, making it a potential target for novel anti-tuberculosis drugs. This study used enzyme-coupled fluorescence to examine the stability of MtSK stored in 50% glycerol at -30 ℃, 4 ℃, and ±28 ℃ for six days. Results showed stable enzyme activity values (α=0.05) at all temperatures. This research underscores that MtSK’s stability depends on its molecular properties, including GC content, hydrophobic residues, Mg2+ binding, and intra-helical salt bridge. Despite some activity decline over time due to glycerol-induced aggregation, MtSK can be safely transported at ±28 ℃ for up to six days without special cooling compartment. Understanding MtSK stability ensures its active conformation remains consistent, reducing off-target effects on drug design and enhancing drug efficacy. This insight ultimately leads to high-quality and commercially viable tuberculosis treatment development. Future research should explore MtSK stability at higher temperatures and assess the optimal glycerol content for cryopreservation.

Article Details

How to Cite
Wibowo, A., Komariyah, T., Prabandari, E. E., Ariyani, T., & Siska, E. (2024). TEMPERATURE EFFECTS ON THE STABILITY OF MYCOBACTERIUM TUBERCULO-SIS SHIKIMATE KINASE (MtSK): STRATEGIES FOR SECURE TRANSPORT. Jurnal Bioteknologi Dan Biosains Indonesia, 11(1), 106–120. Retrieved from https://ejournal.brin.go.id/JBBI/article/view/5751
Section
Articles

References

Alhaji Isa M (2020) Virtual Screening, Mo-lecular Docking and Dynamic Simula-tion of Shikimate Kinase from Myco-bacterium Tuberculosis Using in Silico Approach

Anchordoquy TJ, Izutsu KI, Randolph TW, Carpenter JF (2001) Maintenance of Quaternary Structure in the Frozen State Stabilizes Lactate Dehydrogen-ase during Freeze–Drying. Arch Bio-chem Biophys 390:35–41. https://doi.org/10.1006/ABBI.2001.2351

Bentley R, Sc Referee D, Haslam E The Shikimate Pathway-A Metabolic Tree with Many Branches

Bradford MM (1976) A rapid and sensitive method for the quantitation of mi-crogram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254. https://doi.org/10.1016/0003-2697(76)90527-3

Braham SA, Siar EH, Arana-Peña S, Ba-vandi H, Carballares D, Morellon-Sterling R, de Andrades D, Kornecki JF, Fernandez-Lafuente R (2021) Positive effect of glycerol on the sta-bility of immobilized enzymes: Is it a universal fact? Process Biochemistry 102:108–121. https://doi.org/10.1016/j.procbio.2020.12.015

Che Hussian CHA, Leong WY (2023) Thermostable enzyme research ad-vances: a bibliometric analysis. Jour-nal of Genetic Engineering and Bio-technology 21

Chen X, Bhandari B, Zhou P (2019) Insight into the effect of glycerol on stability of globular proteins in high protein model system. Food Chem 278:780–785. https://doi.org/10.1016/J.FOODCHEM.2018.11.117

Cheng F, Ma Y, Uzzi B, Loscalzo J (2020) Importance of scientific collaboration in contemporary drug discovery and development: a detailed network analysis. BMC Biol 18. https://doi.org/10.1186/s12915-020-00868-3

Correia C, Tavares E, Lopes C, Silva JG, Duarte A, Geraldes V, Rodrigues MA, Melo EP (2020) Stability of Protein Formulations at Subzero Tempera-tures by Isochoric Cooling. J Pharm Sci 109:316–322. https://doi.org/10.1016/j.xphs.2019.06.017

Cowan JA (2002) Structural and catalytic chemistry of magnesium-dependent enzymes

Das R, Gerstein M (2000) The stability of thermophilic proteins: A study based on comprehensive genome compari-son. Funct Integr Genomics 1:76–88. https://doi.org/10.1007/s101420000003

Dias MVB, Faím LM, Vasconcelos IB, De Oliveira JS, Basso LA, Santos DS, De Azevedo WF (2007) Effects of the magnesium and chloride ions and shi-kimate on the structure of shikimate kinase from Mycobacterium tubercu-losis. Acta Crystallogr Sect F Struct Biol Cryst Commun 63:1–6. https://doi.org/10.1107/S1744309106046823

Freitas de Freitas T, Roth CD, Abbadi BL, Hopf FSM, Perelló MA, de Matos Czeczot A, de Souza EV, Borsoi AF, Machado P, Bizarro CV, Basso LA, Timmers LFSM (2023) Identification of potential inhibitors of Mycobacterium tuberculosis shikimate kinase: molec-ular docking, in silico toxicity and in vitro experiments. J Comput Aided Mol Des 37:117–128. https://doi.org/10.1007/s10822-022-00495-w

Goodenough PW, Jenkins JA (1991) Pro-tein engineering to change thermal stability for food enzymes

Gordon S, Simithy J, Goodwin DC, Calde-rón AI (2015) Selective mycobacte-rium tuberculosis shikimate kinase in-hibitors as potential antibacterials. Perspect Medicin Chem 7:9–20. https://doi.org/10.4137/PMC.S13212

Hartuti ED, Inaoka DK, Komatsuya K, Miya-zaki Y, Miller RJ, Xinying W, Sadikin M, Prabandari EE, Waluyo D, Kuroda M, Amalia E, Matsuo Y, Nugroho NB, Saimoto H, Pramisandi A, Watanabe YI, Mori M, Shiomi K, Balogun EO, Shiba T, Harada S, Nozaki T, Kita K (2018) Biochemical studies of mem-brane bound Plasmodium falciparum mitochondrial L-malate:quinone oxi-doreductase, a potential drug target. Biochim Biophys Acta Bioenerg 1859:191–200. https://doi.org/10.1016/j.bbabio.2017.12.004

Hickey DA, Singer GA (2004) Genomic and proteomic adaptations to growth at high temperature What’s so special about adaptation to growth at high temperature?

Hirai M, Ajito S, Sugiyama M, Iwase H, Ta-kata S ichi, Shimizu N, Igarashi N, Martel A, Porcar L (2018) Direct Evi-dence for the Effect of Glycerol on Protein Hydration and Thermal Struc-tural Transition. Biophys J 115:313–327. https://doi.org/10.1016/j.bpj.2018.06.005

Imamura RM, Kumagai K, Nakano H, Oka-be T, Nagano T, Kojima H (2019) In-expensive High-Throughput Screen-ing of Kinase Inhibitors Using One-Step Enzyme-Coupled Fluorescence Assay for ADP Detection. SLAS Dis-covery 24:284–294. https://doi.org/10.1177/2472555218810139

Izutsu K-I, Yoshioka S, Terao T Stabilizing Effect of Amphiphilic Excipients on the Freeze-Thawing and Freeze-Drying of Lactate Dehydrogenase

Kawamoto S, Hori C, Taniguchi H, Okubo S, Aoki S (2023) Identification of novel antimicrobial compounds targeting Mycobacterium tuberculosis shikimate kinase using in silico hierarchical structure-based drug screening. Tu-berculosis 141. https://doi.org/10.1016/j.tube.2023.102362

Khoshnevisan G, Emamzadeh R, Nazari M, Rasa SMM, Sariri R, Hassani L (2018) Kinetics, structure, and dynam-ics of Renilla luciferase solvated in bi-nary mixtures of glycerol and water and the mechanism by which glycerol obstructs the enzyme emitter site. Int J Biol Macromol 117:617–624. https://doi.org/10.1016/J.IJBIOMAC.2018.05.160

Knape MJ, Ahuja LG, Bertinetti D, Burghardt NCG, Zimmermann B, Tay-lor SS, Herberg FW (2015) Divalent Metal Ions Mg2+ and Ca2+ Have Dis-tinct Effects on Protein Kinase A Ac-tivity and Regulation. ACS Chem Biol 10:2303–2315. https://doi.org/10.1021/acschembio.5b00271

Koradi R, Billeter M, Wiithrich K (1996) MOLMOL: A program for display and analysis of macromolecular structures

Kumar V, Chari R, Sharma VK, Kalonia DS (2011) Modulation of the thermody-namic stability of proteins by polyols: Significance of polyol hydrophobicity and impact on the chemical potential of water. Int J Pharm 413:19–28. https://doi.org/10.1016/J.IJPHARM.2011.04.011

Lane BL (1925) Freezing points of glycerol and its aqueous solutions. Armour soap works

Leiden HAK (1940) Physica VII, no 4 Brownian motion in a field of force and the diffusion model of chemical reac-tions

Li WF, Zhou XX, Lu P (2005) Structural fea-tures of thermozymes. Biotechnol Adv 23:271–281

Macarrón R, Hertzberg RP (2009) Design and implementation of high-throughput screening assays. Meth-ods Mol Biol 565:1–32. https://doi.org/10.1007/978-1-60327-258-2_1

Meng FG, Hong YK, He HW, Lyubarev AE, Kurganov BI, Yan Y Bin, Zhou HM (2004) Osmophobic Effect of Glycerol on Irreversible Thermal Denaturation of Rabbit Creatine Kinase. Biophys J 87:2247–2254. https://doi.org/10.1529/BIOPHYSJ.104.044784

Moisă ME, Amariei DA, Nagy EZA, Szarvas N, Toșa MI, Paizs C, Bencze LC (2020) Fluorescent enzyme-coupled activity assay for phenylalanine am-monia-lyases. Sci Rep 10. https://doi.org/10.1038/s41598-020-75474-y

Nurkanto A, Imamura R, Rahmawati Y, Prabandari EE, Waluyo D, Annoura T, Yamamoto K, Sekijima M, Nishimura Y, Okabe T, Shiba T, Shibata N, Kojima H, Duffy J, Nozaki T (2022) Dephospho-Coenzyme A Kinase Is an Exploitable Drug Target against Plasmodium falciparum: Identification of Selective Inhibitors by High-Throughput Screening of a Large Chemical Compound Library. Antimi-crob Agents Chemother 66. https://doi.org/10.1128/aac.00420-22

Papaneophytou CP, Grigoroudis AI, McIn-nes C, Kontopidis G (2014) Quantifi-cation of the effects of ionic strength, viscosity, and hydrophobicity on pro-tein-ligand binding affinity. ACS Med Chem Lett 5:931–936. https://doi.org/10.1021/ml500204e

Pazhang M, Mehrnejad F, Pazhang Y, Falahati H, Chaparzadeh N (2016) Ef-fect of sorbitol and glycerol on the stability of trypsin and difference be-tween their stabilization effects in the various solvents. Biotechnol Appl Bio-chem 63:206–213. https://doi.org/10.1002/bab.1366

Rahul Reddy MB, Krishnasamy SK, Kathiravan MK (2020) Identification of novel scaffold using ligand and struc-ture based approach targeting shiki-mate kinase. Bioorg Chem 102. https://doi.org/10.1016/j.bioorg.2020.104083

Rajput VS, Mehra R, Kumar S, Nargotra A, Singh PP, Khan IA (2016) Screening of antitubercular compound library identifies novel shikimate kinase in-hibitors of Mycobacterium tuberculo-sis. Appl Microbiol Biotechnol 100:5415–5426. https://doi.org/10.1007/s00253-015-7268-8

Rigoldi F, Donini S, Redaelli A, Parisini E, Gautieri A (2018) Review: Engineer-ing of thermostable enzymes for in-dustrial applications. APL Bioeng 2

Romero CM, Albis A (2010) Influence of polyols and glucose on the surface tension of bovine α-lactalbumin in aqueous solution. In: Journal of Solu-tion Chemistry. pp 1865–1876

Schaudien D, Baumga¨rtner W, Herden C (2007) High Preservation of DNA Standards Diluted in 50% Glycerol

Sharma S, Vaid S, Bhat B, Singh S, Bajaj BK (2019) Thermostable Enzymes for Industrial Biotechnology. In: Advances in Enzyme Technology, First Edition. Elsevier, pp 469–495

Simithy J, Fuanta NR, Alturki M, Hobrath J V., Wahba AE, Pina I, Rath J, Hamann MT, Deruiter J, Goodwin DC, Calderón AI (2018a) Slow-Binding In-hibition of Mycobacterium tuberculosis Shikimate Kinase by Manzamine Al-kaloids. Biochemistry 57:4923–4933. https://doi.org/10.1021/acs.biochem.8b00231

Simithy J, Fuanta NR, Hobrath J V., Kochanowska-Karamyan A, Hamann MT, Goodwin DC, Calderón AI (2018b) Mechanism of irreversible in-hibition of Mycobacterium tuberculosis shikimate kinase by ilimaquinone. Bi-ochim Biophys Acta Proteins Proteom 1866:731–739. https://doi.org/10.1016/j.bbapap.2018.04.007

Simithy J, Reeve N, Hobrath J V, Reynolds RC, Calderón AI (2014) Identification of shikimate kinase inhibitors among anti-Mycobacterium tuberculosis compounds by LC-MS. Tuberculosis 94:152–158. https://doi.org/https://doi.org/10.1016/j.tube.2013.12.004

Sissi C, Palumbo M (2009) Effects of mag-nesium and related divalent metal ions in topoisomerase structure and function. Nucleic Acids Res 37:702–711. https://doi.org/10.1093/nar/gkp024

Tiwari A, Bhat R (2006) Stabilization of yeast hexokinase A by polyol osmo-lytes: Correlation with the physico-chemical properties of aqueous solu-tions. Biophys Chem 124:90–99. https://doi.org/10.1016/j.bpc.2006.06.003

Uribe S, Sampedro JG (2003a) Measuring Solution Viscosity and its Effect on Enzyme Activity

Uribe S, Sampedro JG (2003b) Measuring Solution Viscosity and its Effect on Enzyme Activity (2023) Global tuber-culosis report 2023

Most read articles by the same author(s)