Molecular docking of Subtilisin K2, a fibrin-degrading enzyme from Indonesian moromi, with its substrates

Syahbanu, Fathma; Giriwono, Puspo Edi; Tjandrawinata, Raymond R.; Suhartono, Maggy Thenawidjaja

doi:10.1590/fst.61820

Cited by 4 publications

(4 citation statements)

References 32 publications

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“…Generally, molecular docking consists of four stages: selection and preparation of protein structures, preparation of ligands, docking, and analysis of results (Figure 4) (Tu et al, 2018). Several softwares can be used to analyze molecular docking, such as AutoDock Vina, AutoDock 4.0, GRIDock, MdockPep, Tag-Dock, Schrodinger, GOLD, DOT, and so on (FitzGerald et al, 2020, Syahbanu et al, 2022. Various studies have used molecular docking in selecting the bioactive peptide from foods to illustrate the biological mechanism, such as the study of antithrombotic peptides from milk proteins (Tu et al, 2018), antimicrobial peptides from milk (Liu et al, 2015), DPP-IV inhibitor peptide from spinach seed protein, ACE inhibitor peptides from kefir and edible rhizomes (Sompinit et al, 2020), and antimicrobial peptides produced by Streptomyces (Kurnianto et al, 2021).…”

Section: Molecular Dockingmentioning

confidence: 99%

Prospects of bioinformatics approach for exploring and mapping potential bioactive peptide of Rusip (The traditional Indonesian fermented anchovy): A Review

Alfid Kurnianto,

Syahbanu,

Hamidatun

et al. 2023

AFSSAAE

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Rusip is a traditional Indonesian side-dishes food that is a fermented anchovy product originating from Bangka Belitung. During the fermentation, various lactic acid bacteria grew in rusip and produced bioactive peptides because of proteolytic enzyme action. Several treatments to obtain bioactive peptides can be conducted (fermentation, in vivo digestion, and in vitro hydrolysis using enzymes). The in vivo and in vitro methods are a widely used approach, but these methods are costly and time-consuming. These limitations could be solved by the bioinformatics approach. This method manages and interprets information about biological systems that employ computational methods. This study aimed to review recent studies on rusip and similar fermented fish and peptide bioactive with their bioactivity), steps, advantages, and limitations of bioactive peptide studies using the bioinformatics approach. The review article was written using narrative literature review method, which based on in-depth investigation from scientific literatures by identifing keywords, reviewing the content of articles, and synthesizing the findings. The results showed that using bioinformatics has provided opportunities for the development of bioactive peptides. Through this method, bioactive peptide identification begins with determining the main sample protein and the enzymes in protein hydrolysis. The further steps are protein hydrolysis simulation, determining the potential for bioactivity, and molecular docking. The bioinformatics analyses were performed synergistically to predict the protein or peptide characteristics from the sample and its bioactivity and determine its interaction with their receptor. However, despite the advantages, the bioinformatics approach also has several limitations, such as the lack of certain types of proteins or peptides in the database and hydrolysis simulation tool. Combining conventional and in silico methods (hybrid method) is potential to obtain the new and promising bioactive peptides from rusip and other fermented fish (i.e., budu, bekasam, and pla duk ra) and meat products for development product, both functional food and supplements.

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Section: Molecular Dockingmentioning

confidence: 99%

Prospects of bioinformatics approach for exploring and mapping potential bioactive peptide of Rusip (The traditional Indonesian fermented anchovy): A Review

Alfid Kurnianto,

Syahbanu,

Hamidatun

et al. 2023

AFSSAAE

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“…Residue PHE117 on the Aα chain, LEU121 and TRP125 on the Bβ chain, and ASP53, PHE54, and THR57 on the γ chain [39].…”

Section: Subtilisin K2mentioning

confidence: 99%

Computational Prediction of the Interaction of Ivermectin with Fibrinogen

Vottero

Tavernini

Santin

et al. 2023

IJMS

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Hypercoagulability and formation of extensive and difficult-to-lyse microclots are a hallmark of both acute COVID-19 and long COVID. Fibrinogen, when converted to fibrin, is responsible for clot formation, but abnormal structural and mechanical clot properties can lead to pathologic thrombosis. Recent experimental evidence suggests that the spike protein (SP) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may directly bind to the blood coagulation factor fibrinogen and induce structurally abnormal blood clots with heightened proinflammatory activity. Accordingly, in this study, we used molecular docking and molecular dynamics simulations to explore the potential activity of the antiparasitic drug ivermectin (IVM) to prevent the binding of the SARS-CoV-2 SP to fibrinogen and reduce the occurrence of microclots. Our computational results indicate that IVM may bind with high affinity to multiple sites on the fibrinogen peptide, with binding more likely in the central, E region, and in the coiled-coil region, as opposed to the globular D region. Taken together, our in silico results suggest that IVM may interfere with SP–fibrinogen binding and, potentially, decrease the formation of fibrin clots resistant to degradation. Additional in vitro studies are warranted to validate whether IVM binding to fibrinogen is sufficiently stable to prevent interaction with the SP, and potentially reduce its thrombo-inflammatory effect in vivo.

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“…Plasmin akan memotong bekuan fibrin atau trombus menjadi produk degradasi fibrin yang selanjutnya akan dimetabolisme oleh hati dan ginjal (Gambar 2). Kelompok protein yang diketahui sebagai thrombin activated fibrinolysis inhibitor (TAFI) juga menghambat kerja plasmin melalui pemotongan residu lisin pada fibrin yang dibutuhkan plasmin sebagai sisi mediasi untuk fibrinolisis (Wolberg, 2007) Bacillus subtilis K2 Moromi Indonesia - (Syahbanu et al, 2020a, Syahbanu et al, 2020b, Syahbanu et al, 2022 penghambat aktivator plasminogen-2 (PAI-2) hanya bekerja menghambat urokinase, serta α2penghambat plasmin (α2-PI) yang bekerja menghambat plasmin (Cesarman-Maus dan Hajjar, 2005).…”

Section: Mekanisme Pembekuan Darah Dan Sistem Fibrinolisisunclassified

Kajian Enzim Fibrinolitik pada Mikroorganisme Asal Pangan Fermentasi Asia: Review

Syahbanu

Pawestri

2023

J. Teknol. Hasil. Pertanian

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<em><span>Data collected by WHO in 2019 shows an estimated 17.9 million (equivalent to 32% of global death). The total number is due to cardiovascular disease, 85% were due to heart attacks and strokes. One of the basic pathophysiologies of stroke is atero-thromboembolic (thrombosis). The accumulation of clots formed by fibrin in blood vessels can inhibit several processes in the body system, such as blood flow, oxygen transportation, and transportation of nutritional and non-nutritional compounds needed. Fibrinolytic enzymes from food microbes have attracted attention for further research as thrombolytic agents. The Bacillus genus from fermented foods can produce strong fibrinolytic enzymes, such as Bacillus natto from natto (Japan), Bacillus subtilis KCK-7 from Chungkook-jang (Korea), Bacillus weihenstephanensis from shrimp paste (Vietnam), Bacillus amyloliquefaciens MH18B1 from Hawaijar (India), Rhizopus chinensis 12 from Chinese wine (China), and Bacillus pumillus and Bacillus subtilis K2 from fermented soybean food products such as tempe gembus, red oncom, and moromi (Indonesia). The high protein content in soybeans can be used as a medium for the growth of proteolytic and fibrinolytic microorganisms. Studies in Asia regarding fibrinolytic enzymes from fermented foods are still limited, even though the Asian region comprises many countries rich in fermented foods. This review is relevant to healthy food ingredients from local fermented foods. Recently, microbial fibrinolytic enzymes from fermented foods have received tremendous interest in the medical field. Many local fermented foods are a potential source of fibrin-degrading enzymes, which can be further developed to treat diseases like stroke and heart attack. This article aims to review microbial fibrinolytic enzymes from various fermented foods and their impact on health, especially thrombosis. This manuscript review uses the narrative review method. From the overall discussion, it can be concluded that fermented foods have properties as fibrinolytic agents.</span></em>

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Molecular docking of Subtilisin K2, a fibrin-degrading enzyme from Indonesian moromi, with its substrates

Cited by 4 publications

References 32 publications

Prospects of bioinformatics approach for exploring and mapping potential bioactive peptide of Rusip (The traditional Indonesian fermented anchovy): A Review

Prospects of bioinformatics approach for exploring and mapping potential bioactive peptide of Rusip (The traditional Indonesian fermented anchovy): A Review

Computational Prediction of the Interaction of Ivermectin with Fibrinogen

Kajian Enzim Fibrinolitik pada Mikroorganisme Asal Pangan Fermentasi Asia: Review

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