TRPA1 modulation by piperidine carboxamides suggests an evolutionarily conserved binding site and gating mechanism

Significance The TRPA1 channel functions as an irritant sensor and is a therapeutic target for treating pain, itch, and respiratory diseases. TRPA1 can be activated by electrophilic compounds via covalent modification or activated by noncovalent agonists via ligand binding. However, how covalent modification leads to channel opening and, importantly, how noncovalent binding activates TRPA1 are not well-understood. Here we identified a group of noncovalent agonists and used them to explore TRPA1 gating through iterative functional analyses, molecular modeling, and structure–activity relationship studies. We show that TRPA1 possesses an evolutionarily conserved ligand binding site common to other TRP channels. The combination of computational modeling and experimental structure–activity data lays the foundations for rational drug design. The transient receptor potential ankyrin 1 (TRPA1) channel functions as an irritant sensor and is a therapeutic target for treating pain, itch, and respiratory diseases. As a ligand-gated channel, TRPA1 can be activated by electrophilic compounds such as allyl isothiocyanate (AITC) through covalent modification or activated by noncovalent agonists through ligand binding. However, how covalent modification leads to channel opening and, importantly, how noncovalent binding activates TRPA1 are not well-understood. Here we report a class of piperidine carboxamides (PIPCs) as potent, noncovalent agonists of human TRPA1. Based on their species-specific effects on human and rat channels, we identified residues critical for channel activation; we then generated binding modes for TRPA1–PIPC interactions using structural modeling, molecular docking, and mutational analysis. We show that PIPCs bind to a hydrophobic site located at the interface of the pore helix 1 (PH1) and S5 and S6 transmembrane segments. Interestingly, this binding site overlaps with that of known allosteric modulators, such as A-967079 and propofol. Similar binding sites, involving π-helix rearrangements on S6, have been recently reported for other TRP channels, suggesting an evolutionarily conserved mechanism. Finally, we show that for PIPC analogs, predictions from computational modeling are consistent with experimental structure–activity studies, thereby suggesting strategies for rational drug design.

[1]  L. Hammett,et al.  The Effect of Structure Upon the Reactions of Organic Compounds. Temperature and Solvent Influences , 1936 .

[2]  L. Hammett The Effect of Structure upon the Reactions of Organic Compounds. Benzene Derivatives , 1937 .

[3]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[4]  R. Friesner,et al.  Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides† , 2001 .

[5]  Peter McIntyre,et al.  ANKTM1, a TRP-like Channel Expressed in Nociceptive Neurons, Is Activated by Cold Temperatures , 2003, Cell.

[6]  A. Patapoutian,et al.  Noxious Cold Ion Channel TRPA1 Is Activated by Pungent Compounds and Bradykinin , 2004, Neuron.

[7]  Hege S. Beard,et al.  Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. , 2004, Journal of medicinal chemistry.

[8]  D. McKemy,et al.  Mustard oils and cannabinoids excite sensory nerve fibres through the TRP channel ANKTM1 , 2004, Nature.

[9]  Matthew P. Repasky,et al.  Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. , 2004, Journal of medicinal chemistry.

[10]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[11]  M. Caterina,et al.  5-Iodoresiniferatoxin Evokes Hypothermia in Mice and Is a Partial Transient Receptor Potential Vanilloid 1 Agonist in Vitro , 2005, Journal of Pharmacology and Experimental Therapeutics.

[12]  Beiying Liu,et al.  Functional Recovery from Desensitization of Vanilloid Receptor TRPV1 Requires Resynthesis of Phosphatidylinositol 4,5-Bisphosphate , 2005, The Journal of Neuroscience.

[13]  Clifford J. Woolf,et al.  TRPA1 Contributes to Cold, Mechanical, and Chemical Nociception but Is Not Essential for Hair-Cell Transduction , 2006, Neuron.

[14]  David Julius,et al.  TRPA1 Mediates the Inflammatory Actions of Environmental Irritants and Proalgesic Agents , 2006, Cell.

[15]  D. Julius,et al.  TRP channel activation by reversible covalent modification , 2006, Proceedings of the National Academy of Sciences.

[16]  R. Friesner,et al.  Novel procedure for modeling ligand/receptor induced fit effects. , 2006, Journal of medicinal chemistry.

[17]  Tom Halgren,et al.  New Method for Fast and Accurate Binding‐site Identification and Analysis , 2007, Chemical biology & drug design.

[18]  Jeremy R. Greenwood,et al.  Epik: a software program for pKa prediction and protonation state generation for drug-like molecules , 2007, J. Comput. Aided Mol. Des..

[19]  Michael Zhao,et al.  TRPA1 mediates formalin-induced pain , 2007, Proceedings of the National Academy of Sciences.

[20]  Peter G. Schultz,et al.  Noxious compounds activate TRPA1 ion channels through covalent modification of cysteines , 2007, Nature.

[21]  T. Holzman,et al.  Activation of TRPA1 Channels by the Fatty Acid Amide Hydrolase Inhibitor 3′-Carbamoylbiphenyl-3-yl cyclohexylcarbamate (URB597) , 2007, Molecular Pharmacology.

[22]  A. Basbaum,et al.  4-Hydroxynonenal, an endogenous aldehyde, causes pain and neurogenic inflammation through activation of the irritant receptor TRPA1 , 2007, Proceedings of the National Academy of Sciences.

[23]  M. Schaefer,et al.  TRPA1 Is Differentially Modulated by the Amphipathic Molecules Trinitrophenol and Chlorpromazine* , 2007, Journal of Biological Chemistry.

[24]  D. Massi,et al.  Cigarette smoke-induced neurogenic inflammation is mediated by alpha,beta-unsaturated aldehydes and the TRPA1 receptor in rodents. , 2008, The Journal of clinical investigation.

[25]  A. Patapoutian,et al.  Identification of Transmembrane Domain 5 as a Critical Molecular Determinant of Menthol Sensitivity in Mammalian TRPA1 Channels , 2008, The Journal of Neuroscience.

[26]  P. Hajduk,et al.  Molecular Determinants of Species-Specific Activation or Blockade of TRPA1 Channels , 2008, The Journal of Neuroscience.

[27]  T. Neelands,et al.  Transient receptor potential A1 mediates an osmotically activated ion channel , 2008, The European journal of neuroscience.

[28]  Roland L. Dunbrack,et al.  proteins STRUCTURE O FUNCTION O BIOINFORMATICS Improved prediction of protein side-chain conformations with SCWRL4 , 2022 .

[29]  Cristian Micheletti,et al.  MISTRAL: a tool for energy-based multiple structural alignment of proteins , 2009, Bioinform..

[30]  Thomas A. Halgren,et al.  Identifying and Characterizing Binding Sites and Assessing Druggability , 2009, J. Chem. Inf. Model..

[31]  G. Bedoya,et al.  A Gain-of-Function Mutation in TRPA1 Causes Familial Episodic Pain Syndrome , 2010, Neuron.

[32]  J. Segreti,et al.  Selective blockade of TRPA1 channel attenuates pathological pain without altering noxious cold sensation or body temperature regulation , 2011, PAIN.

[33]  Alexander D. MacKerell,et al.  Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. , 2012, Journal of chemical theory and computation.

[34]  M. Tominaga,et al.  Identification of Molecular Determinants for a Potent Mammalian TRPA1 Antagonist by Utilizing Species Differences , 2013, Journal of Molecular Neuroscience.

[35]  Chaohong Sun,et al.  Species differences and molecular determinant of TRPA1 cold sensitivity , 2013, Nature Communications.

[36]  S. Jordt,et al.  TRPA1 controls inflammation and pruritogen responses in allergic contact dermatitis , 2013, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[37]  Jing Zhang,et al.  Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences , 2013 .

[38]  Woody Sherman,et al.  Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments , 2013, Journal of Computer-Aided Molecular Design.

[39]  D. Julius,et al.  TRPV1 structures in distinct conformations reveal mechanisms of activation , 2013, Nature.

[40]  E. Lumpkin,et al.  The Ion Channel TRPA1 Is Required for Chronic Itch , 2013, The Journal of Neuroscience.

[41]  Andrej Sali,et al.  Comparative Protein Structure Modeling Using MODELLER , 2014, Current protocols in bioinformatics.

[42]  Cass,et al.  UV-Metric, pH-Metric and RP-HPLC Methods to Evaluate the Multiple pKa Values of a Polyprotic Basic Novel Antimalarial Drug Lead, Cyclen Bisquinoline , 2014 .

[43]  M. Tominaga,et al.  Molecular Basis Determining Inhibition/Activation of Nociceptive Receptor TRPA1 Protein , 2014, The Journal of Biological Chemistry.

[44]  D. Julius,et al.  Structure of the TRPA1 ion channel suggests regulatory mechanisms , 2015, Nature.

[45]  D. Julius,et al.  Structure of the TRPA1 ion channel suggests regulatory mechanisms , 2015, Nature.

[46]  M. Klein,et al.  Comparative sequence analysis suggests a conserved gating mechanism for TRP channels , 2015, The Journal of general physiology.

[47]  Jun Chen,et al.  TRPA1 as a drug target—promise and challenges , 2015, Naunyn-Schmiedeberg's Archives of Pharmacology.

[48]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using MODELLER , 2016, Current protocols in bioinformatics.

[49]  J. Warmus,et al.  The discovery of a potent series of carboxamide TRPA1 antagonists , 2016 .

[50]  V. Carnevale,et al.  Voltage-Gated Sodium Channels: Evolutionary History and Distinctive Sequence Features. , 2016, Current topics in membranes.

[51]  D. Julius,et al.  TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action , 2016, Nature.

[52]  Xueming Li,et al.  Cryo-EM Structures of the Human Endolysosomal TRPML3 Channel in Three Distinct States , 2017, Nature Structural & Molecular Biology.

[53]  Ara M. Abramyan,et al.  Identification of a putative binding site critical for general anesthetic activation of TRPA1 , 2017, Proceedings of the National Academy of Sciences.

[54]  Xueming Li,et al.  Structural basis of Ca2+/pH dual regulation of the endolysosomal TRPML1 channel , 2017, Nature Structural &Molecular Biology.

[55]  B. Garcia,et al.  Sites Contributing to TRPA1 Activation by the Anesthetic Propofol Identified by Photoaffinity Labeling. , 2017, Biophysical journal.

[56]  G. Blobel,et al.  Human TRPML1 channel structures in open and closed conformations , 2017, Nature.

[57]  Z. Zhou,et al.  Structural basis of TRPV5 channel inhibition by econazole revealed by cryo-EM , 2017, Nature Structural & Molecular Biology.

[58]  V. Carnevale,et al.  Computational Approaches to Studying Voltage-Gated Ion Channel Modulation by General Anesthetics. , 2018, Methods in enzymology.

[59]  E. C. Twomey,et al.  Opening of the Human Epithelial Calcium Channel TRPV6 , 2017, Nature.

[60]  Gabriel C Lander,et al.  Structure of the cold- and menthol-sensing ion channel TRPM8 , 2017, Science.

[61]  M. Klein,et al.  A consistent picture of TRPV1 activation emerges from molecular simulations and experiments , 2018, bioRxiv.

[62]  M. Klein,et al.  Ion Channel Sensing: Are Fluctuations the Crux of the Matter? , 2018, The journal of physical chemistry letters.

[63]  Fan Yang,et al.  Molecular basis for heat desensitization of TRPV1 ion channels , 2019, Nature Communications.