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1. Design and synthesis of diazine-based panobinostat analogues for HDAC8 inhibition

   https://doi.org/10.3762/bjoc.16.59  

   Balasubramaniam, Sivaraman ; Vijayan, Sajith ; Goldman, Liam V ; May, Xavier A ; Dodson, Kyra ; Adhikari, Sweta ; Rivas, Fatima ; Watkins, Davita L ; Stoddard, Shana V ( January 2020 , Beilstein Journal of Organic Chemistry)

   null (Ed.)

   Guided by computational analysis, herein we report the design, synthesis and evaluation of four novel diazine-based histone deacetylase inhibitors (HDACis). The targets of interest (TOI) are analogues of panobinostat, one of the most potent and versatile HDACi reported. By simply replacing the phenyl core of panobinostat with that of a diazine derivative, docking studies against HDAC2 and HDAC8 revealed that the four analogues exhibit inhibition activities comparable to that of panobinostat. Multistep syntheses afforded the visualized targets TOI1 , TOI2 , TOI3-rev and TOI4 whose biological evaluation confirmed the strength of HDAC8 inhibition with TOI4 displaying the greatest efficacy at varying concentrations. The results of this study lay the foundation for future design strategies toward more potent HDACis for HDAC8 isozymes and further therapeutic applications for neuroblastoma. 

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2. Structural basis of AMPA receptor inhibition by trans ‐4‐butylcyclohexane carboxylic acid

   https://doi.org/10.1111/bph.15254  

   Yelshanskaya, Maria V. ; Singh, Appu K. ; Narangoda, Chamali ; Williams, Robin S. B. ; Kurnikova, Maria G. ; Sobolevsky, Alexander I. ( October 2020 , British Journal of Pharmacology)

   AMPA receptors, which shape excitatory postsynaptic currents and are directly involved in overactivation of synaptic function during seizures, represent a well‐accepted target for anti‐epileptic drugs. Trans‐4‐butylcyclohexane carboxylic acid (4‐BCCA) has emerged as a new promising anti‐epileptic drug in several in vitro and in vivo seizure models, but the mechanism of its action remained unknown. The purpose of this study is to characterize structure and dynamics of 4‐BCCA interaction with AMPA receptors.

   We studied the molecular mechanism of AMPA receptor inhibition by 4‐BCCA using a combination of X‐ray crystallography, mutagenesis, electrophysiological assays, and molecular dynamics simulations.

   We identified 4‐BCCA binding sites in the transmembrane domain (TMD) of AMPA receptor, at the lateral portals formed by transmembrane segments M1–M4. At this binding site, 4‐BCCA is very dynamic, assumes multiple poses, and can enter the ion channel pore.

   4‐BCCA represents a low‐affinity inhibitor of AMPA receptors that acts at the TMD sites distinct from non‐competitive inhibitors, such as the anti‐epileptic drug perampanel and the ion channel blockers. Further studies might examine the possibsility of synergistic use of these inhibitors in treatment of epilepsy and a wide range of neurological disorders and gliomas.

   This article is part of a themed issue on Structure Guided Pharmacology of Membrane Proteins (BJP 75th Anniversary). To view the other articles in this section visithttp://onlinelibrary.wiley.com/doi/10.1111/bph.v179.14/issuetoc

    

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3. Allosteric discrimination at the NADH/ADP regulatory site of glutamate dehydrogenase

   https://doi.org/10.1002/pro.3748  

   Nassar, Omneya M. ; Wong, Ka‐Yiu ; Lynch, Gillian C. ; Smith, Thomas J. ; Pettitt, B. Montgomery ( November 2019 , Protein Science)

   Glutamate dehydrogenase (GDH) is a target for treating insulin‐related disorders, such as hyperinsulinism hyperammonemia syndrome. Modeling native ligand binding has shown promise in designing GDH inhibitors and activators. Our computational investigation of the nicotinamide adenine diphosphate hydride (NADH)/adenosine diphosphate (ADP) site presented in this paper provides insight into the opposite allosteric effects induced at a single site of binding inhibitor NADH versus activator ADP to GDH. The computed binding free‐energy difference between NADH and ADP using thermodynamic integration is −0.3 kcal/mol, which is within the −0.275 and −1.7 kcal/mol experimental binding free‐energy difference range. Our simulations show an interesting model of ADP with dissimilar binding conformations at each NADH/ADP site in the GDH trimer, which explains the poorly understood strong binding but weak activation shown in experimental studies. In contrast, NADH showed similar inhibitory binding conformations at each NADH/ADP site. The structural analysis of the important residues in the NADH/ADP binding site presented in this paper may provide potential targets for mutation studies for allosteric drug design.

    

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4. Biophysical Rationale for the Selective Inhibition of PTP1B over TCPTP by Nonpolar Terpenoids

   https://doi.org/10.1021/acs.jpcb.3c03791  

   Friedman, Anika J. ; Padgette, Hannah M. ; Kramer, Levi ; Liechty, Evan T. ; Donovan, Gregory W. ; Fox, Jerome M. ; Shirts, Michael R. ( October 2023 , The Journal of Physical Chemistry B)

   Protein tyrosine phosphatases (PTPs) are emerging drug targets for many diseases, including cancer, autoimmunity, and neurological disorders. A high degree of structural similarity between their catalytic domains, however, has hindered the development of selective pharmacological agents. Our previous research uncovered two unfunctionalized terpenoid inhibitors that selectively inhibit PTP1B over T-cell PTP (TCPTP), two PTPs with high sequence conservation. Here, we use molecular modeling, with supporting experimental validation, to study the molecular basis of this unusual selectivity. Molecular dynamics (MD) simulations suggest that PTP1B and TCPTP share a h-bond network that connects the active site to a distal allosteric pocket; this network stabilizes the closed conformation of the catalytically essential WPD loop, which it links to the L–11 loop and neighboring α3 and α7 helices on the other side of the catalytic domain. Terpenoid binding to either of two proximal C-terminal sites─an α site and a β site─can disrupt the allosteric network; however, binding to the α site forms a stable complex only in PTP1B. In TCPTP, two charged residues disfavor binding at the α site in favor of binding at the β site, which is conserved between the two proteins. Our findings thus indicate that minor amino acid differences at the poorly conserved α site enable selective binding, a property that might be enhanced with chemical elaboration, and illustrate more broadly how minor differences in the conservation of neighboring─yet functionally similar─allosteric sites can affect the selectivity of inhibitory scaffolds (e.g., fragments). 

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5. Sex-dependent transcription of cardiac electrophysiology and links to acetylation modifiers based on the GTEx database

   https://doi.org/10.3389/fcvm.2022.941890  

   Pressler, Michael P. ; Horvath, Anelia ; Entcheva, Emilia ( July 2022 , Frontiers in Cardiovascular Medicine)

   Development of safer drugs based on epigenetic modifiers, e.g., histone deacetylase inhibitors (HDACi), requires better understanding of their effects on cardiac electrophysiology. Using RNAseq data from the genotype-tissue-expression database (GTEx), we created models that link the abundance of acetylation enzymes (HDAC/SIRT/HATs), and the gene expression of ion channels (IC) via select cardiac transcription factors (TFs) in male and female adult human hearts (left ventricle, LV). Gene expression data (transcripts per million, TPM) from GTEx donors (21–70 y.o.) were filtered, normalized and transformed to Euclidian space to allow quantitative comparisons in 84 female and 158 male LVs. Sex-specific partial least-square (PLS) regression models, linking gene expression data for HDAC/SIRT/HATs to TFs and to ICs gene expression, revealed tight co-regulation of cardiac ion channels by HDAC/SIRT/HATs, with stronger clustering in the male LV. Co-regulation of genes encoding excitatory and inhibitory processes in cardiac tissue by the acetylation modifiers may help explain their predominantly net-neutral effects on cardiac electrophysiology. ATP1A1 , encoding for the Na/K pump, represented an outlier—with orthogonal regulation by the acetylation modifiers to most of the ICs. The HDAC/SIRT/HAT effects were mediated by strong (+) TF regulators of ICs, e.g., MEF2A and TBX5 , in both sexes. Furthermore, for male hearts, PLS models revealed a stronger (+/-) mediatory role on ICs for NKX25 and TGF1B/KLF4 , respectively, while RUNX1 exhibited larger (-) TF effects on ICs in females. Male-trained PLS models of HDAC/SIRT/HAT effects on ICs underestimated the effects on some ICs in females. Insights from the GTEx dataset about the co-expression and transcriptional co-regulation of acetylation-modifying enzymes, transcription factors and key cardiac ion channels in a sex-specific manner can help inform safer drug design. 

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