Protegrin-2, a potential inhibitor for targeting SARS-CoV-2 main protease Mpro

Jan, Zainab; Geethakumari, Anupriya M.; Biswas, Kabir H.; Jithesh, Puthen Veettil

doi:10.1016/j.csbj.2023.07.020

Cited by 3 publications

(2 citation statements)

References 45 publications

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“…Importantly, BRET efficiency varies inversely with the sixth power of the distance between the donor and the acceptor, and thus, a small increase in the distance between the two results in a large decrease in the BRET efficiency. We successfully used this technique to develop highly sensitive and specific biosensors ( Biswas et al, 2008 ; Biswas and Visweswariah, 2011 ; Biswas and Visweswariah, 2017 ; Geethakumari et al, 2022b ), including one for monitoring SARS-CoV-2 main protease activity ( Geethakumari et al, 2022a ; Moovarkumudalvan et al, 2022 ; Jan et al, 2023 ). For engineering a BRET-based oligonucleotide detection platform (biosensors) for SARS-CoV-2 parental and Delta variants, we explored the utilization of both Gaussia luciferase (GLuc) and NanoLuc (NLuc) luciferase as the energy donor and utilized NLuc due to its high bioluminescence that will aid in the utilization of the biosensor in a point-of-care diagnostics tool.…”

Section: Introductionmentioning

confidence: 99%

BRET-based biosensors for SARS-CoV-2 oligonucleotide detection

Sultana,

Geethakumari,

Islam

et al. 2024

Front. Bioeng. Biotechnol.

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The need for the early detection of emerging pathogenic viruses and their newer variants has driven the urgent demand for developing point-of-care diagnostic tools. Although nucleic acid-based methods such as reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and loop-mediated isothermal amplification (LAMP) have been developed, a more facile and robust platform is still required. To address this need, as a proof-of-principle study, we engineered a prototype—the versatile, sensitive, rapid, and cost-effective bioluminescence resonance energy transfer (BRET)-based biosensor for oligonucleotide detection (BioOD). Specifically, we designed BioODs against the SARS-CoV-2 parental (Wuhan strain) and B.1.617.2 Delta variant through the conjugation of specific, fluorescently modified molecular beacons (sensor module) through a complementary oligonucleotide handle DNA functionalized with the NanoLuc (NLuc) luciferase protein such that the dissolution of the molecular beacon loop upon the binding of the viral oligonucleotide will result in a decrease in BRET efficiency and, thus, a change in the bioluminescence spectra. Following the assembly of the BioODs, we determined their kinetics response, affinity for variant-specific oligonucleotides, and specificity, and found them to be rapid and highly specific. Furthermore, the decrease in BRET efficiency of the BioODs in the presence of viral oligonucleotides can be detected as a change in color in cell phone camera images. We envisage that the BioODs developed here will find application in detecting viral infections with variant specificity in a point-of-care-testing format, thus aiding in large-scale viral infection surveillance.

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Section: Introductionmentioning

confidence: 99%

BRET-based biosensors for SARS-CoV-2 oligonucleotide detection

Sultana,

Geethakumari,

Islam

et al. 2024

Front. Bioeng. Biotechnol.

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“…Harnkit et al studied the docking and molecular dynamics (MD) of AVP candidates targeting the Mpro [50]. These studies provide a range of perspectives on the interactions between peptides and Mpro, by exploring their possible therapeutic applications [51–53].…”

Section: Introductionmentioning

confidence: 99%

Antiviral peptides inhibiting the main protease of SARS‐CoV‐2 investigated by computational screening and in vitro protease assay

Stewart,

Shawon,

Ali

et al. 2023

Journal of Peptide Science

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The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) plays an important role in viral replication and transcription and received great attention as a vital target for drug/peptide development. Therapeutic agents such as small‐molecule drugs or peptides that interact with the Cys–His present in the catalytic site of Mpro are an efficient way to inhibit the protease. Although several emergency‐approved vaccines showed good efficacy and drastically dropped the infection rate, evolving variants are still infecting and killing millions of people globally. While a small‐molecule drug (Paxlovid) received emergency approval, small‐molecule drugs have low target specificity and higher toxicity. Besides small‐molecule drugs, peptide therapeutics are thus gaining increasing popularity as they are easy to synthesize and highly selective and have limited side effects. In this study, we investigated the therapeutic value of 67 peptides targeting Mpro using molecular docking. Subsequently, molecular dynamics (MD) simulations were implemented on eight protein–peptide complexes to obtain molecular‐level information on the interaction between these peptides and the Mpro active site, which revealed that temporin L, indolicidin, and lymphocytic choriomeningitis virus (LCMV) GP1 are the best candidates in terms of stability, interaction, and structural compactness. These peptides were synthesized using the solid‐phase peptide synthesis protocol, purified by reversed‐phase high‐performance liquid chromatography (RP‐HPLC), and authenticated by mass spectrometry (MS). The in vitro fluorometric Mpro activity assay was used to validate the computational results, where temporin L and indolicidin were observed to be very active against SARS‐CoV‐2 Mpro with IC50 values of 38.80 and 87.23 μM, respectively. A liquid chromatography–MS (LC–MS) assay was developed, and the IC50 value of temporin L was measured at 23.8 μM. The solution‐state nuclear magnetic resonance (NMR) structure of temporin L was determined in the absence of sodium dodecyl sulfate (SDS) micelles and was compared to previous temporin structures. This combined investigation provides critical insights and assists us to further develop peptide inhibitors of SARS‐CoV‐2 Mpro through structural guided investigation.

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Engineering β-catenin-derived peptides for α-catenin binding

Uddin,

Rasool,

Geethakumari

et al. 2024

emergent mater.

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The complex formed by the β-catenin and α-catenin adaptor proteins acts as a molecular bridge that enables E-cadherin-based cell–cell adhesion assembly and maintenance in the epithelial tissue. This occurs through the interaction between the intracellular domain of E-cadherin and β-catenin on the one hand and between F-actin and α-catenin on the other hand. In addition to its role in cell–cell adhesion formation, it has been reported that E-cadherin mediates breast cancer cell metastasis to distant organs. Therefore, development of biomaterials such as peptides with ability to modulate the interaction between β-catenin and α-catenin presents an opportunity to modulate cell–cell adhesion. Here, we have performed computational and experimental analysis to develop β-catenin-derived peptides with the ability to bind α-catenin. Specifically, we analyzed the available β- and α-catenin complex structure and identified residues on β-catenin having potential to form new interactions upon mutation. We tested the wild-type (WT) and mutant β-catenin-derived peptides for their binding to α-catenin using conventional and steered molecular dynamics simulations, revealing an increased interaction of P128E and M131E mutant peptides. We then designed a Bioluminescence Resonance Energy Transfer (BRET)-based assay to monitor binding of the β-catenin-derived peptides with α-catenin, which revealed similar binding affinities of the WT and mutant β-catenin-derived peptides. Further, expression of the WT and the M131E mutant peptide resulted in a change in the aspect ratio of the cells suggestive of their ability to affect cell–cell adhesion. We envisage that the β-catenin-derived peptides engineered here will find application in blocking the interaction between β-catenin and α-catenin and, thus, modulate E-cadherin adhesion, which may lead to potential therapeutic avenue in abrogating E-cadherin-mediated metastasis of invasive breast cancer cells.

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Protegrin-2, a potential inhibitor for targeting SARS-CoV-2 main protease Mpro

Cited by 3 publications

References 45 publications

BRET-based biosensors for SARS-CoV-2 oligonucleotide detection

BRET-based biosensors for SARS-CoV-2 oligonucleotide detection

Antiviral peptides inhibiting the main protease of SARS‐CoV‐2 investigated by computational screening and in vitro protease assay

Engineering β-catenin-derived peptides for α-catenin binding

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