A Critical Observation on the Design and Development of Reported Peptide Inhibitors of DENV NS2B-NS3 Protease in the Last Two Decades

: Dengue is one of the neglected tropical diseases, which remains a reason for concern as cases seem to rise every year. The failure of the only dengue vaccine, Dengvaxia®, has made the problem more severe and humanity has no immediate respite from this global burden. Dengue virus (DENV) NS2B-NS3 protease is an attractive target partly due to its role in polyprotein processing. Also, since it is among the most conserved domains in the viral genome, it could produce a broad scope of opportunities toward antiviral drug discovery in general. This review has made a detailed analysis of each case of the design and development of peptide inhibitors against DENV NS2B-NS3 protease in the last two decades. Also, we have discussed the reasons attributed to their inhibitory activity, and wherever possible, we have highlighted the concerns raised, challenges met, and suggestions to improve the inhibitory activity. Thus, we attempt to take the readers through the designing and development of reported peptide inhibitors and gain insight from these developments, which could further contribute toward strategizing the designing and development of peptide inhibitors of DENV protease with improved properties in the coming future.

Download Full-text

Potential Dual Role of West Nile Virus NS2B in Orchestrating NS3 Enzymatic Activity in Viral Replication

Viruses ◽

10.3390/v13020216 ◽

2021 ◽

Vol 13 (2) ◽

pp. 216

Author(s):

Alanna C. Tseng ◽

Vivek R. Nerurkar ◽

Kabi R. Neupane ◽

Helmut Kae ◽

Pakieli H. Kaufusi

Keyword(s):

West Nile Virus ◽

Enzymatic Activity ◽

Nonstructural Protein ◽

Antiviral Drug ◽

West Nile ◽

Biochemical Assays ◽

In Trans ◽

Viral Polyprotein ◽

Ns3 Protease

West Nile virus (WNV) nonstructural protein 3 (NS3) harbors the viral triphosphatase and helicase for viral RNA synthesis and, together with NS2B, constitutes the protease responsible for polyprotein processing. NS3 is a soluble protein, but it is localized to specialized compartments at the rough endoplasmic reticulum (RER), where its enzymatic functions are essential for virus replication. However, the mechanistic details behind the recruitment of NS3 from the cytoplasm to the RER have not yet been fully elucidated. In this study, we employed immunofluorescence and biochemical assays to demonstrate that NS3, when expressed individually and when cleaved from the viral polyprotein, is localized exclusively to the cytoplasm. Furthermore, NS3 appeared to be peripherally recruited to the RER and proteolytically active when NS2B was provided in trans. Thus, we provide evidence for a potential additional role for NS2B in not only serving as the cofactor for the NS3 protease, but also in recruiting NS3 from the cytoplasm to the RER for proper enzymatic activity. Results from our study suggest that targeting the interaction between NS2B and NS3 in disrupting the NS3 ER localization may be an attractive avenue for antiviral drug discovery.

Download Full-text

Multiple polymerase acidic (PA) I38X substitutions in influenza A(H1N1)pdm09 virus permit polymerase activity and cause reduced baloxavir inhibition

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkaa527 ◽

2020 ◽

Author(s):

Jeremy C Jones ◽

Philippe N Q Pascua ◽

Walter N Harrington ◽

Richard J Webby ◽

Elena A Govorkova

Keyword(s):

Inhibitory Activity ◽

Influenza A ◽

Antiviral Drug ◽

Polymerase Activity ◽

Resistance Marker ◽

Complex Activity ◽

Replication Complex ◽

Virus Rescue ◽

Influenza A H1n1 ◽

Targeted Approach

Abstract Background Baloxavir marboxil is an antiviral drug that targets the endonuclease activity of the influenza virus polymerase acidic (PA) protein. PA I38T/M/F substitutions reduce its antiviral efficacy. Objectives To understand the effects of the 19 possible amino acid (AA) substitutions at PA 38 on influenza A(H1N1)pdm09 polymerase activity and inhibition by baloxavir acid, the active metabolite of baloxavir marboxil. Methods Influenza A(H1N1)pdm09 viral polymerase complexes containing all 19 I38X AA substitutions were reconstituted in HEK293T cells in a mini-replicon assay. Polymerase complex activity and baloxavir inhibitory activity were measured in the presence or absence of 50 nM baloxavir acid. Results Only three substitutions (R, K, P) reduced polymerase activity to <79% of I38-WT. When compared with the prototypical baloxavir marboxil resistance marker T38, 5 substitutions conferred 10%–35% reductions in baloxavir acid inhibitory activity (M, L, F, Y, C) and 11 substitutions conferred >50% reductions (R, K, S, N, G, W, A, Q, E, D, H), while two substitutions (V, P) maintained baloxavir acid inhibitory activity. Conclusions Most PA 38 substitutions permit a functional replication complex retaining some drug resistance in the mini-replicon assay. This study provides a targeted approach for virus rescue and analysis of novel baloxavir marboxil reduced-susceptibility markers, supports the consideration of a broader range of these markers during antiviral surveillance and adds to the growing knowledge of baloxavir marboxil resistance profiles.

Download Full-text

Potential of Peptide-Based Non-Structural Protein 1 (NS1) Inhibitor in Obstructing Dengue Virus (DENV) Replication

Green Medical Journal ◽

10.33096/gmj.v3i1.71 ◽

2021 ◽

Vol 3 (1) ◽

pp. 1-12

Author(s):

Muhammad Mikail Athif Zhafir Asyura ◽

Ahmad Fauzi ◽

Fakhru Adlan Ayub

Keyword(s):

Dengue Virus ◽

Viral Replication ◽

Dengue Fever ◽

Immune Cells ◽

Viral Protein ◽

Viral Genome ◽

Antiviral Drug ◽

Ns1 Protein ◽

Humoral Immune ◽

Stimulation Of

Introduction: Dengue Virus (DENV) is the pathogen for human dengue fever and is responsible for 390 million infections per year. The viral genome produces about 10 viral protein products, one of them being NS1. The NS1 protein plays a key role in viral replication and stimulation of humoral immune cells, thus being the perfect candidate to create an effective antiviral drug or vaccine for dengue Methods: Dengue Virus (DENV) is the pathogen for human dengue fever and is responsible for 390 million infections per year. The viral genome produces about 10 viral protein products, one of them being NS1. The NS1 protein plays a key role in viral replication and stimulation of humoral immune cells, thus being the perfect candidate to create an effective antiviral drug or vaccine for dengue Conclusion: The review established promising results of using peptide-based intervention on NS1. Further in vivo and randomized controlled trials are advised to solidify the applicability and biosafety of the intervention

Download Full-text

Targeting viral genome synthesis as broad-spectrum approach against RNA virus infections

Antiviral Chemistry and Chemotherapy ◽

10.1177/2040206620976786 ◽

2020 ◽

Vol 28 ◽

pp. 204020662097678

Author(s):

Johanna Huchting

Keyword(s):

Broad Spectrum ◽

Viral Genome ◽

De Novo ◽

Rna Viruses ◽

Rna Virus ◽

Antiviral Drug ◽

Building Blocks ◽

Structural Features ◽

Pathogen Transmission ◽

Nucleotide Synthesis

Zoonotic spillover, i.e. pathogen transmission from animal to human, has repeatedly introduced RNA viruses into the human population. In some cases, where these viruses were then efficiently transmitted between humans, they caused large disease outbreaks such as the 1918 flu pandemic or, more recently, outbreaks of Ebola and Coronavirus disease. These examples demonstrate that RNA viruses pose an immense burden on individual and public health with outbreaks threatening the economy and social cohesion within and across borders. And while emerging RNA viruses are introduced more frequently as human activities increasingly disrupt wild-life eco-systems, therapeutic or preventative medicines satisfying the “one drug-multiple bugs”-aim are unavailable. As one central aspect of preparedness efforts, this review digs into the development of broadly acting antivirals via targeting viral genome synthesis with host- or virus-directed drugs centering around nucleotides, the genomes’ universal building blocks. Following the first strategy, selected examples of host de novo nucleotide synthesis inhibitors are presented that ultimately interfere with viral nucleic acid synthesis, with ribavirin being the most prominent and widely used example. For directly targeting the viral polymerase, nucleoside and nucleotide analogues (NNAs) have long been at the core of antiviral drug development and this review illustrates different molecular strategies by which NNAs inhibit viral infection. Highlighting well-known as well as recent, clinically promising compounds, structural features and mechanistic details that may confer broad-spectrum activity are discussed. The final part addresses limitations of NNAs for clinical development such as low efficacy or mitochondrial toxicity and illustrates strategies to overcome these.

Download Full-text

3,5-Bis((E)-4-methoxybenzylidene)-1-(2-morpholinoethyl)piperidin-4-one

Molbank ◽

10.3390/m1159 ◽

2020 ◽

Vol 2020 (4) ◽

pp. M1159

Author(s):

Tyas Kuswardani ◽

Noval Herfindo ◽

Neni Frimayanti ◽

Rudi Hendra ◽

Adel Zamri

Keyword(s):

Mass Spectrometry ◽

Inhibitory Activity ◽

Title Compound ◽

Chemical Structure ◽

Ns3 Protease

The 3,5-bis((E)-4-methoxybenzylidene)-1-(2-morpholinoethyl)piperidin-4-one (3) compound was synthesized by a two-step reaction with 92% yield. The chemical structure of compound 3 was confirmed by IR, NMR, and mass spectrometry. The title compound was screened for its anti-dengue activity against DENV2 NS2B-NS3 protease and showed 39.09% inhibitory activity at 200 µg/mL.

Download Full-text

The flavivirus NS2B–NS3 protease–helicase as a target for antiviral drug development

Antiviral Research ◽

10.1016/j.antiviral.2015.03.014 ◽

2015 ◽

Vol 118 ◽

pp. 148-158 ◽

Cited By ~ 128

Author(s):

Dahai Luo ◽

Subhash G. Vasudevan ◽

Julien Lescar

Keyword(s):

Drug Development ◽

Antiviral Drug ◽

Ns3 Protease

Download Full-text

Potent Peptide Inhibitors of Human Hepatitis C Virus NS3 Protease Are Obtained by Optimizing the Cleavage Products

Biochemistry ◽

10.1021/bi980314n ◽

1998 ◽

Vol 37 (25) ◽

pp. 8906-8914 ◽

Cited By ~ 127

Author(s):

Paolo Ingallinella ◽

Sergio Altamura ◽

Elisabetta Bianchi ◽

Marina Taliani ◽

Raffaele Ingenito ◽

...

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Peptide Inhibitors ◽

Human Hepatitis ◽

Ns3 Protease

Download Full-text

Human Immunodeficiency Virus Type 1 Escape from RNA Interference

Journal of Virology ◽

10.1128/jvi.77.21.11531-11535.2003 ◽

2003 ◽

Vol 77 (21) ◽

pp. 11531-11535 ◽

Cited By ~ 293

Author(s):

Daniel Boden ◽

Oliver Pusch ◽

Frederick Lee ◽

Lynne Tucker ◽

Bharat Ramratnam

Keyword(s):

Human Immunodeficiency Virus ◽

Rna Interference ◽

Human Immunodeficiency Virus Type ◽

Virus Type ◽

Viral Genome ◽

Antiviral Drug ◽

Selective Inhibition ◽

Immunodeficiency Virus ◽

Hiv 1

ABSTRACT Sequence-specific degradation of mRNA by short interfering RNA (siRNA) allows the selective inhibition of viral proteins that are critical for human immunodeficiency virus type 1 (HIV-1) replication. The aim of this study was to characterize the potency and durability of virus-specific RNA interference (RNAi) in cell lines that stably express short hairpin RNA (shRNA) targeting the HIV-1 transactivator protein gene tat. We found that the antiviral activity of tat shRNA was abolished due to the emergence of viral quasispecies harboring a point mutation in the shRNA target region. Our results suggest that, in order for RNAi to durably suppress HIV-1 replication, it may be necessary to target highly conserved regions of the viral genome. Alternatively, similar to present antiviral drug therapy paradigms, DNA constructs expressing multiple siRNAs need to be developed that target different regions of the viral genome, thereby reducing the probability of generating escape mutants.

Download Full-text

Comparative analysis of the unbinding pathways of antiviral drug Indinavir from HIV and HTLV1 proteases by Supervised Molecular Dynamics simulation

10.1101/2021.03.27.437308 ◽

2021 ◽

Author(s):

Farzin Sohraby ◽

Hassan Aryapour

Keyword(s):

Inhibitory Activity ◽

Antiviral Drug ◽

Good Explanation ◽

Dynamics Simulation ◽

Stacking Interactions ◽

Pi Stacking ◽

Efficacious Treatment ◽

The Stability ◽

Flap Region ◽

Hiv 1

Determining the unbinding pathways of potential small molecule compounds from their target proteins is of great significance for designing efficacious treatment solutions. One of these potential compounds is the approved HIV-1 protease inhibitor, indinavir, which has a weak effect on the HTLV-1 protease. In this work, by employing SuMD method, we reconstructed the unbinding pathways of indinavir from HIV and HTLV-1 proteases in order to compare and to understand the mechanism of the unbinding, and also to discover the reasons for the lack of inhibitory activity of indinavir against the HTLV-1 protease. We achieved multiple unbinding events from both HIV and HTLV-1 proteases in which the RMSD values of indinavir reached over 4 nm. Also, we found that the mobility and the fluctuations of the flap region is higher in the HTLV-1 protease which makes the drug less stable. We realized that critically positioned aromatic residues such as Trp98/Trp98' and Phe67/Phe67' in the HTLV-1 protease can make strong pi-Stacking interactions with indinavir in the unbinding pathway which are unfavorable for the stability of indinavir in the active site. The details found in this study can make a good explanation for the lack of inhibitory activity of this drug against HTLV-1 protease. We believe the details discovered in this work can be a great assist for designing more effective and more selective inhibitors for the HTLV-1 protease.

Download Full-text