SPOP

A team of scientists from Shanghai Institute of Materia Medica, Chinese Academy of Sciences, has proposed a novel approach to drug design, aiming to circumvent the intricate pipeline of protein structure-based drug development. The traditional method commences with the protein sequence, constructs a three-dimensional (3D) structure through structural biology or structure prediction, pinpoints binding pockets, and finally uncovers modulators via virtual screening or de novo design. However, this multi-step procedure has inherent limitations, as each part requires independent optimization. These limitations include the absence of high-resolution structures for numerous proteins, the challenge of accurately predicting active sites, defining binding pockets for novel targets with multiple domains, and anticipating allosteric sites. TransformerCPI2.0: predicting compound protein interaction without using protein structure.Leveraging the power of AI To address these issues, the researchers introduced the sequence-to-drug concept, a method that uncovers modulators straight from protein sequences, eliminating intermediary steps. This concept employs end-to-end differentiable learning, executing the entire learning process in a self-consistent, data-efficient manner, potentially mitigating the error accumulation inherent to complex pipelines. The team designed the TransformerCPI2.0 tool to validate this concept, demonstrating its general applicability across proteins and chemical space. By conducting case studies, the model's learning efficiency was evaluated, and its acquisition of knowledge was confirmed to be in line with expectations, rather than merely showcasing data bias. TransformerCPI2.0 was employed to explore novel potential treatments for challenging targets, namely speckle-type POZ protein (SPOP) and ring finger protein 130 (RNF130), both of which lack existing 3D structures. Furthermore, a potential new target for proton pump inhibitors (PPIs), ADP-ribosylation factor 1 (ARF1), was identified by the researchers. Drug resistance mutation analysis.New hits for challenging drug targetsSPOP is an E3 ubiquitin ligase that plays a critical role in mediating the ubiquitination and degradation of substrate proteins. In ccRCC cells, SPOP is overexpressed and mislocalized to the cytoplasm, leading to decreased levels of its substrates PTEN and DUSP7. This, in turn, causes increased cell proliferation and tumor growth. PTEN and DUSP7 are negative regulators of the oncogenic AKT and ERK signaling pathways. By mediating their degradation, cytoplasmic SPOP in ccRCC cells causes hyperactivation of AKT and ERK, driving cancer progression. Although SPOP is a promising drug target, effective chemical inhibitors have not yet been developed due to challenges with targeting protein-protein interactions.  But now, with the help of TransformerCPI2.0, new breakthroughs are made possible. By virtually screening compounds against SPOP, the researchers identified a top hit - 221C7. This compound contains a distinctive β-lactam ring not seen in prior SPOP inhibitors. 221C7 was experimentally validated to directly bind to SPOP's MATH domain and disrupt its interactions with substrates like PTEN/DUSP7. An optimized analog 230D7 exhibited anti-cancer effects in ccRCC models. Discovering a novel scaffold hit of SPOP.This success with SPOP demonstrates TransformerCPI2.0's ability to discover new inhibitor chemotypes by virtual screening against novel targets, using only sequence information. The researchers further applied TransformerCPI2.0 to find hits against RNF130, an E3 ligase lacking structural data and known binders. A compound iRNF130-63 was discovered and confirmed to directly bind RNF130. New target for an existing drugIn addition, TransformerCPI2.0 could also be used to screen drugs against the entire human proteome, to identify novel protein targets for repurposing applications. Four PPIs were screened against 2,204 proteins in the DrugBank database, and the top scoring interaction was found to be with ARF1. ARF1 is a small G protein involved in cancer stem cell lipid metabolism. Experimental validation showed that the PPIs directly bound and destabilized ARF1, with rabeprazole exhibiting the strongest effects. The binding occurred covalently at cysteine 159 of ARF1, and rabeprazole suppressed ARF1's GTP nucleotide exchange activity, inhibiting its function.  In colon cancer models, rabeprazole reduced ARF1 activity levels, causing lipid droplet accumulation in cancer stem cells and stimulating an anti-tumor immune response. Knockdown of ARF1 prevented rabeprazole's effects on tumor growth and immune activation, confirming that the mechanism is ARF1-dependent. Identifying ARF1 as the new target of PPIs.This study demonstrates the potential of TransformerCPI2.0 to identify novel drug-target interactions to enable repurposing applications, as shown by the discovery of PPIs as ARF1 inhibitors. Targeting ARF1 with PPIs represents a promising new approach to induce anti-cancer immunity. Further evaluation is still needed to assess their potential as ARF1-targeted immunotherapies. Compared to conventional structure-based drug design, the novel approach is attractive because it conducts the entire learning process in a self-consistent and data-efficient manner, potentially avoiding the accumulation of errors in complex pipelines. The proof-of-concept study illustrates that the sequence-to-drug concept provides a promising direction for rational drug design, especially for proteins lacking high-quality 3D structures. The new approach has the potential to enable the discovery of novel treatments for diseases with poorly defined protein targets.   Reference Chen, L., Fan, Z., Chang, J. et al. Sequence-based drug design as a concept in computational drug design. Nat Commun 14, 4217 (2023). 

Caris Life Sciences President, Dr. David Spetzler, to present on blood-based testing during a special session of the AACR Scientist↔Survivor Program® IRVING, Texas, April 14, 2023 /PRNewswire/ -- Caris Life Sciences®(Caris), the leading molecular science and technology company actively developing and delivering innovative solutions to revolutionize healthcare, today announced that the company and partners within the Caris Precision Oncology Alliance™ (POA) will collectively present four studies across 14 tumor types at the 2023 American Association for Cancer Research (AACR) Annual Meeting being held April 14-19, 2023 in Orlando, Florida, at Booth Number 130. Caris President, David Spetzler, M.S., Ph.D., MBA, will also lead an AACR Scientist↔Survivor Program® Special Session from 3:00 – 3:45 p.m. on Sunday, April 16 titled, "Early and Accurate: Leveraging Blood for Reliable Cancer Detection, Monitoring and Therapy Selection." Continue Reading "We are proud of the collaborative abstracts accepted for presentation at AACR, demonstrating the power of Caris' comprehensive molecular profiling and the large-scale collaboration between the growing number of POA sites," said Chadi Nabhan, M.D., MBA, FACP, Chairman of the Caris Precision Oncology Alliance. "The findings represent important observations, particularly in endometrial and prostate cancer, which enhance our understanding of the pathobiology of disease, potentially leading to novel therapeutics." Caris Life Sciences President, Dr. David Spetzler, to present on blood-based testing during a special session Tweet this "At Caris, our goal is to enable clinicians to make the best individualized treatment choices for their patients, researchers to discover new targets, and the biopharmaceutical industry to develop the next breakthrough medicines," said David Spetzler, M.S., Ph.D., MBA, President of Caris. "The diversity of the over 455,000 lifetime cases in Caris' unique AI-driven platform enables us to identify ethnic differences in the molecular and tumor microenvironment. Better understanding of these differences may help reduce ethnic health disparities and improve outcomes in cancer patients." Poster presentations include: Opposing roles of SPOP mutations in human prostate and endometrial cancers. (Poster Number: 937/20) April 16, 1:30 PM – 5:00 PM ET Molecular Characterization of Prostate Cancer Between Hispanic American and Non-Hispanic Whites: Implications for Cancer Ethnic Health Disparities. (Poster Number: 1895/1) April 17, 9:00 AM – 12:30 PM ET Pan-cancer analysis of XPO1 R749Q mutations across 217,570 patients. (Poster Number: 4253/2) April 18, 9:00 AM – 12:30 PM ET The Heterogeneous Immune and Molecular Landscape of Endometrial Cancer Metastases. (Poster Number: 4538/17) April 18, 9:00 AM – 12:30 PM ET Poster and abstract summaries highlighting this research will be available onsite at Caris' Booth Number 130. The full abstracts are available on the AACR website. Marking its 25th anniversary, the AACR Scientist↔Survivor Program® (SSP) is a unique program designed to build bridges and unity among the leaders of the scientific and cancer survivor and patient advocacy communities worldwide. By strengthening communications and forging partnerships between these important communities in the cancer field, the program enhances efforts to accelerate progress in the fight against cancer. Dr. David Spetzler will lead a special interest session at AACR's SSP, highlighting the importance and challenges facing blood-based cancer detection, monitoring and therapy selection and moderated by Anna Barker, Ph.D., FAACR, Chief Strategy Officer at the Lawrence J. Ellison Institute and founder and chair of the AACR Scientist↔Survivor Program®. The Caris Precision Oncology Alliance includes 82 cancer centers and academic institutions in the United States and beyond. These institutions have early access to the extensive database and artificial intelligence platform within Caris to establish evidence-based standards for cancer profiling and molecular testing in oncology. By leveraging the comprehensive genomic, transcriptomic and proteomic data available through Caris molecular profiling, Caris seeks to provide this network with the ability to prioritize therapeutic options and determine which clinical trial opportunities may benefit their patients. POA members are also able to integrate with a growing portfolio of biomarker directed trials sponsored by biopharma. Additionally, as a member of the POA, institutions have access to Caris CODEai™, the most comprehensive data solution in the industry with cancer treatment information and real-world clinical outcomes evidence for over 350,000 patients covering over 1 million data points per patient. About Caris Life Sciences Caris Life Sciences® (Caris) is the leading molecular science and technology company actively developing and delivering innovative solutions to revolutionize healthcare and improve patient outcomes. Through comprehensive molecular profiling (Whole Exome and Whole Transcriptome Sequencing) and the application of advanced artificial intelligence (AI) and machine learning algorithms, Caris has created the large-scale clinico-genomic database and cognitive computing needed to analyze and unravel the molecular complexity of disease. This information provides an unmatched resource and the ideal path forward to conduct the basic, fundamental research to accelerate discovery for detection, diagnosis, monitoring, therapy selection and drug development to improve the human condition. With a primary focus on cancer, Caris' suite of market-leading molecular profiling offerings assesses DNA, RNA and proteins to reveal a molecular blueprint that helps patients, physicians and researchers better detect, diagnose and treat patients. The company's latest advancement, Caris Assure™, is a blood-based, circulating nucleic acids sequencing (cNAS) assay that combines comprehensive molecular analysis (Whole Exome and Whole Transcriptome Sequencing from blood) and serial monitoring – making it the most powerful liquid biopsy assay ever developed. Headquartered in Irving, Texas, Caris has offices in Phoenix, New York, Tokyo, Japan and Basel, Switzerland. Caris or its distributors provide services in the U.S., Europe, Asia and other international markets. To learn more, please visit CarisLifeSciences.com or follow us on LinkedIn. Caris Life Sciences Media Contact: Lisa Burgner [email protected] 214.294.5606 SOURCE Caris Life Sciences

Scientists have captured the 3D structure of SPOP, revealing how mutations in previously unappreciated regions fuel cancer. SPOP is the most mutated protein in prostate cancer and plays a role in endometrial, uterine and other cancers. Despite this importance, how SPOP mutations drive cancer has been incompletely understood. Scientists at St. Jude Children's Research Hospital used cryo-electron microscopy (cryo-EM) to capture the first 3D structure of the entire SPOP assembly. The study, published today in Molecular Cell,revealed previously unknown SPOP interfaces that harbor clusters of cancer-causing mutations. The normal function of SPOP is to control the level of certain proteins within a cell. When SPOP is dysregulated through mutations, it can cause dramatic effects in the cell because protein levels are altered, triggering abnormal behaviors. SPOP may not be the fire that sets cancer ablaze, but if mismanaged, it can light the fuse. "The prostate cancer-associated mutations are well understood," said corresponding author Tanja Mittag, Ph.D., St. Jude Department of Structural Biology. "They are in the substrate-binding site and prevent SPOP from recognizing its substrates. But mutations found in patients with endometrial and other cancers were puzzling. The mutated sites did not seem to be important for SPOP function, at least looking at previous structures." Big picture understanding Determining the 3D structure of SPOP using cryo-EM allowed the researchers to gain insights into the underlying mechanisms that drive the function of this protein both in its normal state and when mutated in cancer. By looking at how the SPOP oligomer assembles, the researchers were able to identify key interactions between regions of the protein, which had not been seen before. These were exactly the regions that are mutated in endometrial cancer. "Once we had the 3D structure of SPOP, we could see that the pieces of the puzzle that had been missing were inherently important for understanding how SPOP functions in cancer," said co-first author Matthew Cuneo, Ph.D., St. Jude Department of Structural Biology. "We were now able to see that what we initially thought to be regions of SPOP without functional importance are actually key to SPOP assembly and biology." One mutation, dramatic effects Previous studies had demonstrated that the SPOP protein assembles into long filaments. However, scientists could tell that the full picture had yet to be uncovered, as certain mutations unexpectedly affected this filament. For example, mutations in the MATH domain [the part of SPOP that binds substrates] affected the propensity of the protein to assemble and hang around in cells. The researchers also observed how a single mutation could dramatically affect how the protein forms filaments. Mutating the interface that locks the MATH domain in place completely changed the assembly of the proteins from a single to a double filament with intertwined MATH domains. Discovering these additional protein interfaces in the filament using cryo-EM helped further explain how SPOP mutations contribute to cancer. "Taking a broader view to look at the full-length protein gave us a deeper understanding of how mutations affect SPOP," said co-first author Brian O'Flynn, Ph.D., St. Jude Department of Structural Biology. "The scale of the change just from one point mutation is huge. It was unexpected to see that." New questions Researchers in the field have already experimented with drugs that target the MATH domain of SPOP. Drugs could now be developed to target specifically the mutant forms of SPOP in endometrial cancer. One of the implications of this work is that one day it might be possible to differentially target SPOP based upon its functional form within the cell. "In addition to the questions that this research answers, what's exciting is that for scientists asking about SPOP, the possibilities have really opened up," O'Flynn added.