Abstract 410: Development of novel, non-toxic rifamycins that reverse drug resistance

Introduction: We have discovered novel non-toxic rifamycins that are extremely potent at sensitizing many drug-resistant cancers, including DLBCL, to standard-of-care chemotherapeutics.

Methods: CHOP-resistant DLBCL cell lines were derived from CHOP-sensitive cells by “on-off” cycles of CHOP treatment, analogous to clinical therapy. The CHOP-resistant cells were used in high-throughput screening of a highly diverse collection of approximately 50,000 drug-like molecules to identify small molecules that reverse CHOP-resistance. The FDA-approved drug, Rifabutin, was identified as a non-cytotoxic compound that potently reversed resistance to CHOP. Structure-Activity-Relationships (SAR) on Rifabutin were conducted, which led to the generation of a new more potent CHOP-chemosensitizing agent, designated RTI.

Results: RTI was highly synergistic with variety of chemotherapeutics, including doxorubicin (DOX), epirubicin, vinblastine, etoposide in drug-resistant NHL cells. Combination therapy of DOX+RTI in mouse xenograft models of DLBCL was much more effective at repressing tumor growth than with DOX alone. RTI lowered the IC90 in a dose-dependent manner in CD20-positive B cells in bone marrow aspirates from both CHOP-naïve and CHOP-relapsed patients, and in a metastatic lymph node. RTI’s PK characteristics are similar to rifabutin, and it exhibited no overt toxicity in mice or pigs at high doses. RTI rapidly induced mitochondrial superoxide, membrane potential, and fission. The superoxide dismutase, FeTCP, antagonized RTI-induced ROS and potentiation of DOX cytotoxicity. RTI reduced the activity of the Nrf-2 antioxidant protein, upregulated proteins involved in the unfolded protein response (UPR), and induced metabolic reprogramming as indicated by Seahorse assays that showed increased glycolysis and decreased oxygen consumption from 3 to 24 hrs.

Conclusions: RTI has a broad spectrum of action in both double- and triple-hit DLBCL and synergizes with many different chemotherapeutics to restore drug sensitivity. RTI-79 works by dramatically increasing intracellular superoxide through redox cycling, triggers UPR, and downregulates Nrf-2 activity. Thus, RTI-79 increases oxidative stress through the squelching of Nrf-2’s ability to respond to chemotherapeutic stress. Since the parent compound, rifabutin, binds to the aryl hydrocarbon receptor (AhR) and modulates its activity, we hypothesize that RTI mediates its unique pleiotropic chemosensitizing mechanism through targeting of AhR, and provides for a broad, safe, and novel approach to treating drug resistant cancers. Ongoing experiments are investigating the effect of RTI on the AhR-signaling pathway and the role it plays in RTI-mediated chemosensitization and potentiation of chemotherapeutics. A clinical trial of companion dogs with CHOP-relapsed DLBCL treated with combination CHOP+RTI is currently in progress.

Citation Format: Steve A. Maxwell, Deeann Wallis, Nian Zhou, Dwight Baker, Seyed H. Mousavi-Fard, Kimberly Loesch, Stacy Galaviz, Liam Guthrie, Thomas Snavely, Qingan Sun, Carolina M. Rojas, David W. Threadgill, Thomas Ioerger, Wen Dong, Gwen Seemann, Theresa W. Fossum, James C. Sacchettini. Development of novel, non-toxic rifamycins that reverse drug resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 410.

Biological Profiling Enables Rapid Mechanistic Classification of Phenotypic Screening Hits and Identification of KatG Activation-Dependent Pyridine Carboxamide Prodrugs With Activity Against Mycobacterium tuberculosis

Compounds with novel modes of action are urgently needed to develop effective combination therapies for the treatment of tuberculosis. In this study, a series of compounds was evaluated for activity against replicating Mycobacterium tuberculosis and Vero cell line toxicity. Fourteen of the compounds with in vitro activities in the low micrometer range and a favorable selectivity index were classified using reporter strains of M. tuberculosis which showed that six interfered with cell wall metabolism and one disrupted DNA metabolism. Counter-screening against strains carrying mutations in promiscuous drug targets argued against DprE1 and MmpL3 as hits of any of the cell wall actives and eliminated the cytochrome bc₁ complex as a target of any of the compounds. Instead, whole-genome sequencing of spontaneous resistant mutants and/or counter-screening against common isoniazid-resistant mutants of M. tuberculosis revealed that four of the six cell wall-active compounds, all pyridine carboxamide analogues, were metabolized by KatG to form InhA inhibitors. Resistance to two of these compounds was associated with mutations in katG that did not confer cross-resistance to isoniazid. Of the remaining seven compounds, low-level resistance to one was associated with an inactivating mutation in Rv0678, the regulator of the MmpS5-MmpL5 system, which has been implicated in non-specific efflux of multiple chemotypes. Another mapped to the mycothiol-dependent reductase, Rv2466c, suggesting a prodrug mechanism of action in that case. The inability to isolate spontaneous resistant mutants to the seven remaining compounds suggests that they act via mechanisms which have yet to be elucidated.

Reinforcement Learning using EEG signals for Therapeutic Use of Music in Emotion Management

Prolonged influence of negative emotions can result in clinical depression or anxiety, and while many prescribed techniques exist, music therapy approaches, coupled with psychotherapy, have shown to help lower depressive symptoms, supplementing traditional treatment approaches. Identifying the appropriate choice of music, therefore, is of utmost importance. Selecting appropriate playlists, however, are challenged by user feedback that may inadvertently select songs that amplify the negative effects. Therefore, this work uses electroencephalogram (EEG) that automatically identifies the emotional impact of music and trains a reinforcement-learning approach to identify an adaptive personalized playlist of music to lead to improved emotional states. This work uses data from 32 users, collected in the publicly available DEAP dataset, to select songs for users that guide them towards joyful emotional states. Using a domain-specific reward-shaping function, a Q-learning agent is able to correctly guide a majority of users to the target emotional states, represented in a common emotion wheel. The average angular error of all users is 57°, with a standard deviation of 2.8 and the target emotional state is achieved.Clinical relevance- Music therapy for improving clinical depression and anxiety can be supplemented by additional emotion-guided music decisions in remote and personal settings by using automated techniques to capture emotional state and identify music that best guides users to target joyful states.

Targeting protein biotinylation enhances tuberculosis chemotherapy

Successful drug treatment for tuberculosis (TB) depends on the unique contributions of its component drugs. Drug resistance poses a threat to the efficacy of individual drugs and the regimens to which they contribute. Biologically and chemically validated targets capable of replacing individual components of current TB chemotherapy are a major unmet need in TB drug development. We demonstrate that chemical inhibition of the bacterial biotin protein ligase (BPL) with the inhibitor Bio-AMS (5'-[N-(d-biotinoyl)sulfamoyl]amino-5'-deoxyadenosine) killed Mycobacterium tuberculosis (Mtb), the bacterial pathogen causing TB. We also show that genetic silencing of BPL eliminated the pathogen efficiently from mice during acute and chronic infection with Mtb Partial chemical inactivation of BPL increased the potency of two first-line drugs, rifampicin and ethambutol, and genetic interference with protein biotinylation accelerated clearance of Mtb from mouse lungs and spleens by rifampicin. These studies validate BPL as a potential drug target that could serve as an alternate frontline target in the development of new drugs against Mtb.

Impact of immunopathology on the antituberculous activity of pyrazinamide

In the 1970s, inclusion of pyrazinamide (PZA) in the drug regimen of tuberculosis (TB) patients for the first 2 mo achieved a drastic reduction of therapy duration. Until now, however, the mechanisms underlying PZA's unique contribution to efficacy have remained controversial, and animal efficacy data vary across species. To understand how PZA kills bacterial populations present in critical lung lesion compartments, we first characterized a rabbit model of active TB, showing striking similarities in lesion types and fates to nonhuman primate models deemed the most appropriate surrogates of human TB. We next employed this model with lesion-centric molecular and bacteriology readouts to demonstrate that PZA exhibits potent activity against Mycobacterium tuberculosis residing in difficult-to-sterilize necrotic lesions. Our data also indicate that PZA is slow acting, suggesting that PZA administration beyond the first 2 mo may accelerate the cure. In conclusion, we provide a pharmacodynamic explanation for PZA's treatment-shortening effect and deliver new tools to dissect the contribution of immune response versus drug at the lesion level.

Identification of a Mycothiol-Dependent Nitroreductase from Mycobacterium tuberculosis

The success of Mycobacterium tuberculosis (Mtb) as a pathogen depends on the redundant and complex mechanisms it has evolved for resisting nitrosative and oxidative stresses inflicted by host immunity. Improving our understanding of these defense pathways can reveal vulnerable points in Mtb pathogenesis. In this study, we combined genetic, structural, computational, biochemical, and biophysical approaches to identify a novel enzyme class represented by Rv2466c. We show that Rv2466c is a mycothiol-dependent nitroreductase of Mtb and can reduce the nitro group of a novel mycobactericidal compound using mycothiol as a cofactor. In addition to its function as a nitroreductase, Rv2466c confers partial protection to menadione stress.

Mutations in pepQ Confer Low-Level Resistance to Bedaquiline and Clofazimine in Mycobacterium tuberculosis

The novel ATP synthase inhibitor bedaquiline recently received accelerated approval for treatment of multidrug-resistant tuberculosis and is currently being studied as a component of novel treatment-shortening regimens for drug-susceptible and multidrug-resistant tuberculosis. In a limited number of bedaquiline-treated patients reported to date, ≥4-fold upward shifts in bedaquiline MIC during treatment have been attributed to non-target-based mutations in Rv0678 that putatively increase bedaquiline efflux through the MmpS5-MmpL5 pump. These mutations also confer low-level clofazimine resistance, presumably by a similar mechanism. Here, we describe a new non-target-based determinant of low-level bedaquiline and clofazimine cross-resistance in Mycobacterium tuberculosis: loss-of-function mutations in pepQ (Rv2535c), which corresponds to a putative Xaa-Pro aminopeptidase. pepQ mutants were selected in mice by treatment with clinically relevant doses of bedaquiline, with or without clofazimine, and were shown to have bedaquiline and clofazimine MICs 4 times higher than those for the parental H37Rv strain. Coincubation with efflux inhibitors verapamil and reserpine lowered bedaquiline MICs against both mutant and parent strains to a level below the MIC against H37Rv in the absence of efflux pump inhibitors. However, quantitative PCR (qPCR) revealed no significant differences in expression of Rv0678, mmpS5, or mmpL5 between mutant and parent strains. Complementation of a pepQ mutant with the wild-type gene restored susceptibility, indicating that loss of PepQ function is sufficient for reduced susceptibility both in vitro and in mice. Although the mechanism by which mutations in pepQ confer bedaquiline and clofazimine cross-resistance remains unclear, these results may have clinical implications and warrant further evaluation of clinical isolates with reduced susceptibility to either drug for mutations in this gene.

Behavioral and transcriptomic profiling of mice null for Lphn3, a gene implicated in ADHD and addiction

Background

The Latrophilin 3 (LPHN3) gene (recently renamed Adhesion G protein‐coupled receptor L3 (ADGRL3)) has been linked to susceptibility to attention deficit/hyperactivity disorder (ADHD) and vulnerability to addiction. However, its role and function are not well understood as there are no known functional variants.

Methods

To characterize the function of this little known gene, we phenotyped Lphn3 null mice. We assessed motivation for food reward and working memory via instrumental responding tasks, motor coordination via rotarod, and depressive‐like behavior via forced swim. We also measured neurite outgrowth of primary hippocampal and cortical neuron cultures. Standard blood chemistries and blood counts were performed. Finally, we also evaluated the transcriptome in several brain regions.

Results

Behaviorally, loss of Lphn3 increases both reward motivation and activity levels. Lphn3 null mice display significantly greater instrumental responding for food than wild‐type mice, particularly under high response ratios, and swim incessantly during a forced swim assay. However, loss of Lphn3 does not interfere with working memory or motor coordination. Primary hippocampal and cortical neuron cultures demonstrate that null neurons display comparatively enhanced neurite outgrowth after 2 and 3 days in vitro. Standard blood chemistry panels reveal that nulls have low serum calcium levels. Finally, analysis of the transcriptome from prefrontal cortical, striatal, and hippocampal tissue at different developmental time points shows that loss of Lphn3 results in genotype‐dependent differential gene expression (DGE), particularly for cell adhesion molecules and calcium signaling proteins. Much of the DGE is attenuated with age, and is consistent with the idea that ADHD is associated with delayed cortical maturation.

Conclusions

Transcriptome changes likely affect neuron structure and function, leading to behavioral anomalies consistent with both ADHD and addiction phenotypes. The data should further motivate analyses of Lphn3 function in the developmental timing of altered gene expression and calcium signaling, and their effects on neuronal structure/function during development.

Comparison of transposon and deletion mutants in Mycobacterium tuberculosis: The case of rv1248c, encoding 2-hydroxy-3-oxoadipate synthase

We compared phenotypes of five strains of Mycobacterium tuberculosis (Mtb) differing in their expression of rv1248c and its product, 2-hydroxy-3-oxoadipate synthase (HOAS), with a focus on carbon source-dependent growth rates and attenuation in mice. Surprisingly, an rv1248c transposon mutant on a CDC1551 background grew differently than an rv1248c deletion mutant on the same background. Moreover, the same rv1248c deletion in two different yet genetically similar strain backgrounds (CDC1551 and H37Rv) gave different phenotypes, though each could be complemented. Whole genome re-sequencing did not provide an obvious explanation for these discrepancies. These observations offer a cautionary lesson about the strength of inference from complementation and sequence analysis, and commend consideration of more complex phenomena than usually contemplated in Mtb, such as epigenetic control.

Functional genomics screening utilizing mutant mouse embryonic stem cells identifies novel radiation-response genes

Elucidating the genetic determinants of radiation response is crucial to optimizing and individualizing radiotherapy for cancer patients. In order to identify genes that are involved in enhanced sensitivity or resistance to radiation, a library of stable mutant murine embryonic stem cells (ESCs), each with a defined mutation, was screened for cell viability and gene expression in response to radiation exposure. We focused on a cancer-relevant subset of over 500 mutant ESC lines. We identified 13 genes; 7 genes that have been previously implicated in radiation response and 6 other genes that have never been implicated in radiation response. After screening, proteomic analysis showed enrichment for genes involved in cellular component disassembly (e.g. Dstn and Pex14) and regulation of growth (e.g. Adnp2, Epc1, and Ing4). Overall, the best targets with the highest potential for sensitizing cancer cells to radiation were Dstn and Map2k6, and the best targets for enhancing resistance to radiation were Iqgap and Vcan. Hence, we provide compelling evidence that screening mutant ESCs is a powerful approach to identify genes that alter radiation response. Ultimately, this knowledge can be used to define genetic variants or therapeutic targets that will enhance clinical therapy.

High-Throughput Differentiation and Screening of a Library of Mutant Stem Cell Clones Defines New Host-Based Genes Involved in Rabies Virus Infection

We used a genomic library of mutant murine embryonic stem cells (ESCs) and report the methodology required to simultaneously culture, differentiate, and screen more than 3,200 heterozygous mutant clones to identify host-based genes involved in both sensitivity and resistance to rabies virus infection. Established neuronal differentiation protocols were miniaturized such that many clones could be handled simultaneously, and molecular markers were used to show that the resultant cultures were pan-neuronal. Next, we used a green fluorescent protein (GFP) labeled rabies virus to develop, validate, and implement one of the first host-based, high-content, high-throughput screens for rabies virus. Undifferentiated cell and neuron cultures were infected with GFP-rabies and live imaging was used to evaluate GFP intensity at time points corresponding to initial infection/uptake and early and late replication. Furthermore, supernatants were used to evaluate viral shedding potential. After repeated testing, 63 genes involved in either sensitivity or resistance to rabies infection were identified. To further explore hits, we used a completely independent system (siRNA) to show that reduction in target gene expression leads to the observed phenotype. We validated the immune modulatory gene Unc13d and the dynein adapter gene Bbs4 by treating wild-type ESCs and primary neurons with siRNA; treated cultures were resistant to rabies infection/replication. Overall, the potential of such in vitro functional genomics screens in stem cells adds additional value to other libraries of stem cells. This technique is applicable to any bacterial or virus interactome and any cell or tissue types that can be differentiated from ESCs.

Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling

Transposon sequencing (TnSeq) is a next-generation deep sequencing-based method to quantitatively assess the composition of complex mutant transposon libraries after pressure from selection. Although this method can be used for any organism in which transposon mutagenesis is possible, this chapter describes its use in Mycobacterium tuberculosis. More specifically, the methods for generating complex libraries through transposon mutagenesis, design of selective pressure, extraction of genomic DNA, amplification and quantification of transposon insertions through next-generation deep sequencing are covered. Determining gene essentiality and statistical analysis on data collected are also discussed.

Synthesis and evaluation of the 2,4-diaminoquinazoline series as anti-tubercular agents

The 2,4-diaminoquinazoline class of compounds has previously been identified as an effective inhibitor of Mycobacterium tuberculosis growth. We conducted an extensive evaluation of the series for its potential as a lead candidate for tuberculosis drug discovery. Three segments of the representative molecule N-(4-fluorobenzyl)-2-(piperidin-1-yl)quinazolin-4-amine were examined systematically to explore structure-activity relationships influencing potency. We determined that the benzylic amine at the 4-position, the piperidine at 2-position and the N-1 (but not N-3) are key activity determinants. The 3-deaza analog retained similar activity to the parent molecule. Biological activity was not dependent on iron or carbon source availability. We demonstrated through pharmacokinetic studies in rats that good in vivo compound exposure is achievable. A representative compound demonstrated bactericidal activity against both replicating and non-replicating M. tuberculosis. We isolated and sequenced M. tuberculosis mutants resistant to this compound and observed mutations in Rv3161c, a gene predicted to encode a dioxygenase, suggesting that the compound may act as a pro-drug.

Crystallographic protein model-building on the web

X-ray crystallography is the most widely used method to determine the 3D structure of protein molecules. One of the most difficult steps in protein crystallography is model-building, which consists of constructing a backbone and then amino acid side chains into an electron density map. Interpretation of electron density maps represents a major bottleneck in protein structure determination pipelines, and thus, automated techniques to interpret maps can greatly improve the throughput. We have developed WebTex, a simple and yet powerful web interface to TEXTAL, a program that automates this process of fitting atoms into electron density maps. TEXTAL can also be downloaded for local installation.

AVAILABILITY

Web interface, downloadable binaries and documentation at http://textal.tamu.edu

Identifying non-crystallographic symmetry in protein electron-density maps: a feature-based approach

Non-crystallographic symmetry (NCS) averaging is a well known method for improving the quality of an electron-density map and thus aiding structure determination. Prior methods of NCS-operator determination based on estimated heavy-atom positions are prone to errors arising from inaccuracies in these coordinates or differences in the relative orientations of domains between molecules. In this paper, two real-space methods to determine NCS relationships from initial electron-density maps are presented. A brute-force method identifies matching regions in a map by local density correlation. A feature-based algorithm uses rotation-invariant features to reduce the computational time taken by the brute-force algorithm by filtering out regions that are likely to have dissimilar density patterns. This makes the feature-based algorithm faster and as accurate as the brute-force approach. Neither method requires the positions of heavy atoms or any information regarding the protein sequence. Both methods have been tested on a diverse range of experimentally phased maps and the correct NCS relationships were accurately identified for almost all of the test cases. The NCS operators obtained by the feature-based algorithm were used to perform NCS averaging and an improvement in map correlation was observed for some cases.

Analysis of diversity of nucleotide and amino acid distributions in the VD and DJ joining regions in Ig heavy chains

Nucleotide fill-in between the germ line V, D and J genes in the H3 loop of immunoglobulins contributes to the diversity of the antibody repertoire. This fill-in process is mediated by terminal deoxynucleotidyl transferase (TdT), which has been widely believed to insert nucleotides in a random fashion. Using a database of 2443 immunoglobulin sequences, we identified the regions of nucleotide fill-in between the V-D and D-J gene regions. We translated the fill-in nucleotides and measured the diversity within the two regions both at the nucleotide and amino acid level. We found that the nucleotide and amino acid distributions that resulted from nucleotide fill-in were in fact not random. Examination of the synonymous substitution rates of nucleotides revealed evidence suggesting that TdT plays a less significant role in generating antibody diversity than previously thought. We observed preferences for polar residues, which are more likely to encourage interaction with ligand than non-polar residues and are often found in loop regions in general. We also observed a preference for the insertion of smaller residues versus larger residues of similar biochemical properties, aiding in loop flexibility. We interpret these findings to reflect the significant influence of biochemical (i.e. folding) constraints and/or binding affinity constraints (at the cellular/selectional level) on the sequence diversity in the H3 region. These constraints act as a filter on the randomness generated by nucleotide addition by TdT, as well as other diversity generating processes such as recombination of VDJ gene segments and somatic mutation. The results of this study suggest that the antibody repertoire might be reduced from what is traditionally believed.