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Toxins
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Advances in Structure-Based Drug Design of Venom Peptides
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Advances in Structure-Based Drug Design of Venom Peptides

A special issue of Toxins (ISSN 2072-6651). This special issue belongs to the section "Animal Venoms".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 15840

Special Issue Editors

Prof. Dr. Owen M. McDougal

E-Mail Website
Guest Editor
Department of Chemistry and Biochemistry, Boise State University, Boise, ID 83725, USA
Interests: conotoxins; Veratrum alkaloids; chemistry and bioactivity of natural products from marine and terrestrial sources; food and dairy chemistry
Special Issues, Collections and Topics in MDPI journals
Dr. Abba Leffler

E-Mail Website
Guest Editor
Drug Discovery Group, Schrödinger, Inc. 120 W. 45th St, New York, NY 10036, USA
Interests: Structure-Based Drug Discovery; Venom Peptides; Free-Energy Perturbation; Ion Channels

Special Issue Information

Dear Colleagues,

Structure-based drug design has become the dominant paradigm for small-molecules. However, its impact on venom peptide therapeutic efforts, while still considerable, has been more limited because of the challenges of obtaining structures of these peptides in complex with their targets, as well as the difficulty of simulating them. Emerging technologies such as cryo-electron microscopy (cryo-EM) for structure determination, graphical processor units (GPUs) for molecular simulation, and free energy methods for potency prediction have the potential to remove these roadblocks. In this Special Issue, our aim is to collect the latest advances in structure-based drug design for venom peptides utilizing these technologies and others. We welcome experimental, theoretical, computational, and interdisciplinary contributions from both academic and industry practitioners.

Prof. Dr. Owen M. McDougal
Dr. Abba Leffler
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a double-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Toxins is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Venom peptide
  • Structure-based drug design
  • Free energy perturbation
  • Ion channel
  • Cryo-electron microscopy
  • Docking

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Published Papers (4 papers)

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Research

13 pages, 1789 KiB  
Article
Expression, Purification and Refolding of a Human NaV1.7 Voltage Sensing Domain with Native-like Toxin Binding Properties
by Ryan V. Schroder, Leah S. Cohen, Ping Wang, Joekeem D. Arizala and Sébastien F. Poget
Toxins 2021, 13(10), 722; https://doi.org/10.3390/toxins13100722 - 12 Oct 2021
Viewed by 3122
Abstract
The voltage-gated sodium channel NaV1.7 is an important target for drug development due to its role in pain perception. Recombinant expression of full-length channels and their use for biophysical characterization of interactions with potential drug candidates is challenging due to the [...] Read more.
The voltage-gated sodium channel NaV1.7 is an important target for drug development due to its role in pain perception. Recombinant expression of full-length channels and their use for biophysical characterization of interactions with potential drug candidates is challenging due to the protein size and complexity. To overcome this issue, we developed a protocol for the recombinant expression in E. coli and refolding into lipids of the isolated voltage sensing domain (VSD) of repeat II of NaV1.7, obtaining yields of about 2 mg of refolded VSD from 1 L bacterial cell culture. This VSD is known to be involved in the binding of a number of gating-modifier toxins, including the tarantula toxins ProTx-II and GpTx-I. Binding studies using microscale thermophoresis showed that recombinant refolded VSD binds both of these toxins with dissociation constants in the high nM range, and their relative binding affinities reflect the relative IC50 values of these toxins for full-channel inhibition. Additionally, we expressed mutant VSDs incorporating single amino acid substitutions that had previously been shown to affect the activity of ProTx-II on full channel. We found decreases in GpTx-I binding affinity for these mutants, consistent with a similar binding mechanism for GpTx-I as compared to that of ProTx-II. Therefore, this recombinant VSD captures many of the native interactions between NaV1.7 and tarantula gating-modifier toxins and represents a valuable tool for elucidating details of toxin binding and specificity that could help in the design of non-addictive pain medication acting through NaV1.7 inhibition. Full article
(This article belongs to the Special Issue Advances in Structure-Based Drug Design of Venom Peptides)
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16 pages, 3069 KiB  
Article
The Allosteric Activation of α7 nAChR by α-Conotoxin MrIC Is Modified by Mutations at the Vestibular Site
by Alican Gulsevin, Roger L. Papke, Clare Stokes, Hue N. T. Tran, Aihua H. Jin, Irina Vetter and Jens Meiler
Toxins 2021, 13(8), 555; https://doi.org/10.3390/toxins13080555 - 10 Aug 2021
Cited by 5 | Viewed by 2777
Abstract
α-conotoxins are 13–19 amino acid toxin peptides that bind various nicotinic acetylcholine receptor (nAChR) subtypes. α-conotoxin Mr1.7c (MrIC) is a 17 amino acid peptide that targets α7 nAChR. Although MrIC has no activating effect on α7 nAChR when applied by itself, it evokes [...] Read more.
α-conotoxins are 13–19 amino acid toxin peptides that bind various nicotinic acetylcholine receptor (nAChR) subtypes. α-conotoxin Mr1.7c (MrIC) is a 17 amino acid peptide that targets α7 nAChR. Although MrIC has no activating effect on α7 nAChR when applied by itself, it evokes a large response when co-applied with the type II positive allosteric modulator PNU-120596, which potentiates the α7 nAChR response by recovering it from a desensitized state. A lack of standalone activity, despite activation upon co-application with a positive allosteric modulator, was previously observed for molecules that bind to an extracellular domain allosteric activation (AA) site at the vestibule of the receptor. We hypothesized that MrIC may activate α7 nAChR allosterically through this site. We ran voltage-clamp electrophysiology experiments and in silico peptide docking calculations in order to gather evidence in support of α7 nAChR activation by MrIC through the AA site. The experiments with the wild-type α7 nAChR supported an allosteric mode of action, which was confirmed by the significantly increased MrIC + PNU-120596 responses of three α7 nAChR AA site mutants that were designed in silico to improve MrIC binding. Overall, our results shed light on the allosteric activation of α7 nAChR by MrIC and suggest the involvement of the AA site. Full article
(This article belongs to the Special Issue Advances in Structure-Based Drug Design of Venom Peptides)
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14 pages, 8268 KiB  
Article
An Smp43-Derived Short-Chain α-Helical Peptide Displays a Unique Sequence and Possesses Antimicrobial Activity against Both Gram-Positive and Gram-Negative Bacteria
by Xudong Luo, Li Ding, Xiangdong Ye, Wen Zhu, Kaiyue Zhang, Fangyan Li, Huiwen Jiang, Zhiwen Zhao and Zongyun Chen
Toxins 2021, 13(5), 343; https://doi.org/10.3390/toxins13050343 - 11 May 2021
Cited by 5 | Viewed by 2949
Abstract
Scorpion venoms are rich resources of antimicrobial peptides (AMPs). While the short-chain noncysteine-containing AMPs have attracted much attention as templates for drug development, the antimicrobial potential of long-chain noncysteine-containing AMPs has been largely overlooked. Here, by using the online HeliQuest server, we designed [...] Read more.
Scorpion venoms are rich resources of antimicrobial peptides (AMPs). While the short-chain noncysteine-containing AMPs have attracted much attention as templates for drug development, the antimicrobial potential of long-chain noncysteine-containing AMPs has been largely overlooked. Here, by using the online HeliQuest server, we designed and analyzed a series of 14-residue fragments of Smp43, a 43-residue long-chain noncysteine-containing AMP identified from the venom of Scorpio maurus palmatus. We found that Smp43(1-14) shows high antimicrobial activity against both Gram-positive and Gram-negative bacteria and is nontoxic to mammalian cells at the antimicrobial dosage. Sequence alignments showed that the designed Smp43(1-14) displays a unique primary structure that is different from other natural short-chain noncysteine-containing AMPs from scorpions, such as Uy17, Uy192 and IsCT. Moreover, the peptide Smp43(1-14) caused concentration-dependent fluorescence increases in the bacteria for all of the tested dyes, propidium iodide, SYTOXTM Green and DiSC3-5, suggesting that the peptide may kill the bacteria through the formation of pore structures in the plasma membrane. Taken together, our work sheds light on a new avenue for the design of novel short-chain noncysteine-containing AMPs and provides a good peptide template with a unique sequence for the development of novel drugs for use against bacterial infectious diseases. Full article
(This article belongs to the Special Issue Advances in Structure-Based Drug Design of Venom Peptides)
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18 pages, 3965 KiB  
Article
Potency-Enhancing Mutations of Gating Modifier Toxins for the Voltage-Gated Sodium Channel NaV1.7 Can Be Predicted Using Accurate Free-Energy Calculations
by Dana Katz, Dan Sindhikara, Michael DiMattia and Abba E. Leffler
Toxins 2021, 13(3), 193; https://doi.org/10.3390/toxins13030193 - 7 Mar 2021
Cited by 11 | Viewed by 5969
Abstract
Gating modifier toxins (GMTs) isolated from venomous organisms such as Protoxin-II (ProTx-II) and Huwentoxin-IV (HwTx-IV) that inhibit the voltage-gated sodium channel NaV1.7 by binding to its voltage-sensing domain II (VSDII) have been extensively investigated as non-opioid analgesics. However, reliably predicting how [...] Read more.
Gating modifier toxins (GMTs) isolated from venomous organisms such as Protoxin-II (ProTx-II) and Huwentoxin-IV (HwTx-IV) that inhibit the voltage-gated sodium channel NaV1.7 by binding to its voltage-sensing domain II (VSDII) have been extensively investigated as non-opioid analgesics. However, reliably predicting how a mutation to a GMT will affect its potency for NaV1.7 has been challenging. Here, we hypothesize that structure-based computational methods can be used to predict such changes. We employ free-energy perturbation (FEP), a physics-based simulation method for predicting the relative binding free energy (RBFE) between molecules, and the cryo electron microscopy (cryo-EM) structures of ProTx-II and HwTx-IV bound to VSDII of NaV1.7 to re-predict the relative potencies of forty-seven point mutants of these GMTs for NaV1.7. First, FEP predicted these relative potencies with an overall root mean square error (RMSE) of 1.0 ± 0.1 kcal/mol and an R2 value of 0.66, equivalent to experimental uncertainty and an improvement over the widely used molecular-mechanics/generalized born-surface area (MM-GB/SA) RBFE method that had an RMSE of 3.9 ± 0.8 kcal/mol. Second, inclusion of an explicit membrane model was needed for the GMTs to maintain stable binding poses during the FEP simulations. Third, MM-GB/SA and FEP were used to identify fifteen non-standard tryptophan mutants at ProTx-II[W24] predicted in silico to have a at least a 1 kcal/mol gain in potency. These predicted potency gains are likely due to the displacement of high-energy waters as identified by the WaterMap algorithm for calculating the positions and thermodynamic properties of water molecules in protein binding sites. Our results expand the domain of applicability of FEP and set the stage for its prospective use in biologics drug discovery programs involving GMTs and NaV1.7. Full article
(This article belongs to the Special Issue Advances in Structure-Based Drug Design of Venom Peptides)
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