Insights from the Molecular modeling, docking analysis of illicit drugs and Bomb Compounds with Honey Bee Odorant Binding Proteins (OBPs)

Kulanthaivel, Langeswaran; Jeyakanthan, Jeyaraman; Mariadasse, Richard; Soorangkattan, Saravanan

doi:10.6026/97320630014219

Cited by 10 publications

(6 citation statements)

References 23 publications

(30 reference statements)

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“…For the plus-C subclass, we identified only one protein (DadjOBP2) that had an identity greater than 90% with DponOBP2a/DponOBP2b and the same motif pattern. Although there is a high identity among closely related species, a high variability of plus-C members among insects has been reported 67 , which coincides with the low similarity (< 45%) between DadjOBP2/DponOBP2 with their homologs in I. typographus and the lack of two motifs in the N-terminus. However, information on the binding affinities of the minus-C and plus-C subfamilies is limited, and members of these families have been reported not only in antennae and labial and maxillary palps but also in nonsensory structures [72][73][74][75][76] ; therefore, additional research is needed on the structure and physiological function of nonclassic OBPs.…”

Section: Discussionmentioning

confidence: 81%

“…However, they have not been identified in any bark beetle transcriptome, even though semiochemicals influence the population dynamics of Dendroctonus species 14,63,64 . In this sense, the results of the phylogenetic reconstruction, in which OBPs with these patterns clustered with proteins from other Coleoptera species that have been classified in a specific PBP/GOBP lineage 49 , suggest the presence of this subgroup of OBPs, so they could be candidates for structural and docking studies with homology models [65][66][67][68] .…”

Section: Discussionmentioning

confidence: 90%

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Identification and motif analyses of candidate nonreceptor olfactory genes of Dendroctonus adjunctus Blandford (Coleoptera: Curculionidae) from the head transcriptome

Torres-Huerta

Segura‐León

Aragón-Magadan

et al. 2020

Sci Rep

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The round-headed pine beetle Dendroctonus adjunctus, whose dispersion and colonization behaviors are linked to a communication system mediated by semiochemicals, is one of the five most critical primary pests in forest ecosystems in Mexico. This study provides the first head transcriptome analysis of D. adjunctus and the identification of the nonreceptor olfactory genes involved in the perception of odors. De novo assembly yielded 44,420 unigenes, and GO annotations were similar to those of antennal transcriptomes of other beetle species, which reflect metabolic processes related to smell and signal transduction. A total of 36 new transcripts of nonreceptor olfactory genes were identified, of which 27 encode OBPs, 7 encode CSPs, and 2 encode SNMP candidates, which were subsequently compared to homologous proteins from other bark beetles and Coleoptera species by searching for sequence motifs and performing phylogenetic analyses. Our study provides information on genes encoding nonreceptor proteins in D. adjunctus and broadens the knowledge of olfactory genes in Coleoptera and bark beetle species, and will help to understand colonization and aggregation behaviors for the development of tools that complement management strategies.

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Section: Discussionmentioning

confidence: 81%

Section: Discussionmentioning

confidence: 90%

Identification and motif analyses of candidate nonreceptor olfactory genes of Dendroctonus adjunctus Blandford (Coleoptera: Curculionidae) from the head transcriptome

Torres-Huerta

Segura‐León

Aragón-Magadan

et al. 2020

Sci Rep

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“…In addition to their abundant expression in insect antennae, some OBP family members are expressed in other tissues, such as the abdomen and wings of Periplaneta americana [ 83 ], and the midgut and head of diamondback moths ( Plutella xylostella ) [ 84 ]. Four OBPs in honeybees are similarly highly expressed in regions with low chemosensory receptor expression [ 85 ]. These cases indicate that OBP may participate in other life activities besides chemosensation, such as responses to adverse environmental conditions and the scavenging of various, small, hydrophobic molecules [ 86 , 87 ].…”

Section: Discussionmentioning

confidence: 99%

Proteomics and ultrastructural analysis of Hermetia illucens (Diptera: Stratiomyidae) larval peritrophic matrix

et al. 2021

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Background The black soldier fly (Hermetia illucens) has significant economic potential. The larvae can be used in financially viable waste management systems, as they are voracious feeders able to efficiently convert low-quality waste into valuable biomass. However, most studies on H. illucens in recent decades have focused on optimizing their breeding and bioconversion conditions, while information on their biology is limited. Methods About 200 fifth instar well-fed larvae were sacrificed in this work. The liquid chromatography-tandem mass spectrometry and scanning electron microscopy were employed in this study to perform a proteomic and ultrastructural analysis of the peritrophic matrix (PM) of H. illucens larvae. Results A total of 565 proteins were identified in the PM samples of H. illucen, of which 177 proteins were predicted to contain signal peptides, bioinformatics analysis and manual curation determined 88 proteins may be associated with the PM, with functions in digestion, immunity, PM modulation, and others. The ultrastructure of the H. illucens larval PM observed by scanning electron microscopy shows a unique diamond-shaped chitin grid texture. Conclusions It is the first and most comprehensive proteomics research about the PM of H. illucens larvae to date. All the proteins identified in this work has been discussed in details, except several unnamed or uncharacterized proteins, which should not be ignored and need further study. A comparison of the ultrastructure between H. illucens larval PM and those of other insects as observed by SEM indicates that the PM displays diverse textures on an ultra-micro scale and we suscept a unique diamond-shaped chitin grid texture may help H. illucens larval to hold more food. This work deepens our understanding of the molecular architecture and ultrastructure of the H. illucens larval PM.

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“…A hybrid DFT approach (B3LYP-Becke's three-parameter exchange potential and the Lee−Yang−Parr correlation functional) was performed for geometry optimization with the basis set of 6−31G**. The energy of the compounds at the aqueous condition was calculated by the Poisson−Boltzmann solver which yielded additional information of about the local and global indices for its reactivity (Langeswaran et al, 2018). Overall, the charge transfer mechanism for the inhibitory reaction of the compounds can be understood by analyzing the HOMO and LUMO molecular orbitals of the receptor-drug binding combinations.…”

Section: Dft Studiesmentioning

confidence: 99%

In silico evaluation of isatin-based derivatives with RNA-dependent RNA polymerase of the novel coronavirus SARS-CoV-2

M¹,

Gideon²,

Mariadasse³

et al. 2020

Preprint

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Isatin (1H-indole-2,3-dione)-containing compounds have been shown to possess several remarkable biological activities. We had previously explored a few isatin-based imidazole derivatives for their predicted dual activity against both inflammation and cancer. We explored 47 different isatin-based derivatives (IBDs) for other potential biological activities using in silico tools and found them to possess anti-viral activity. Using AUTODOCK tools, the binding site, binding energy, inhibitory constant/Ki and receptor-ligand interactions for each of the compounds was analyzed against SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). The partition coefficient (logP) values were predicted using MedChem Designer tool. Based on the best Ki, binding energy and the ideal range of logP (between 1.0-3.0), 10 out of total 47 compounds were deemed to be prospective RdRp inhibitors. Some of these compounds gave better Ki, binding energy and logP values when compared to standard RdRp inhibitors such as remdesivir (Ki = 15.61 μM, logP = 2.2; binding energy = -6.95), a clinically approved RdRp inhibitor which is widely used for critical care of COVID-19 patients. The same in silico parameters were assessed for 9 other popular RdRp inhibitors (other than remdesivir), which were earlier used to target RdRp of other viruses, and are now repurposed to target SARS-CoV-2 RdRp. The results showed that the 10 selected isatin-based derivatives (IBDs) could be further explored for activity against SARS-Cov-2. In the present study we evaluated the efficacy of these compounds in silico.

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Insights from the Molecular modeling, docking analysis of illicit drugs and Bomb Compounds with Honey Bee Odorant Binding Proteins (OBPs)

Cited by 10 publications

References 23 publications

Identification and motif analyses of candidate nonreceptor olfactory genes of Dendroctonus adjunctus Blandford (Coleoptera: Curculionidae) from the head transcriptome

Identification and motif analyses of candidate nonreceptor olfactory genes of Dendroctonus adjunctus Blandford (Coleoptera: Curculionidae) from the head transcriptome

Proteomics and ultrastructural analysis of Hermetia illucens (Diptera: Stratiomyidae) larval peritrophic matrix

In silico evaluation of isatin-based derivatives with RNA-dependent RNA polymerase of the novel coronavirus SARS-CoV-2

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