Biology subjects

Abagyan, R.

Publications and source records attributed to Abagyan, R..

13 recordsLinked to original sources

bioRxiv2026

Pharmacological proximities in the GPCR family discovered using contact-informed amino-acid and binding pocket similarities

Understanding protein proximities in the theoretical ligand space is essential for developing therapeutics with desirable polypharmacology, predicting off-targets, and discovering surrogate ligands for poorly characterized proteins. This is especially important for G protein-coupled receptors (GPCRs) - a major class of drug targets, many of which still lack known ligands. Circumventing this limitation, we present GPCR-CoINPocket v2, a contact-informed metric for detecting GPCR pharmacological similarities from amino-acid sequences alone. We first establish a "gold standard" of pharmacological relatedness using ChEMBL-derived ligand sets. We then replace traditional evolutionary amino acid similarity matrices with a chemically-informed matrix derived from protein:ligand interaction patterns across 3,306 structures, significantly improving early detection of shared pharmacology between distantly homologous receptors. An additional unconstrained, contact-informed matrix further enhances predictive performance. Pilot application of the method revealed previously unrecognized similarities between the {beta}2 adrenoceptor and three Class A peptide GPCRs, which we confirmed experimentally by demonstrating the binding of select ligands of these receptors to the {beta}2. Dimensionality reduction of similarity scores recapitulates known receptor relationships and predicts neighbors of orphan GPCRs later confirmed experimentally. Overall, GPCR-CoINPocket v2 provides a powerful sequence-based framework to prioritize ligand space, predict polypharmacology, and accelerate GPCR drug discovery and deorphanization.

bioinformatics↗

bioRxiv2023

Generative Molecular Design and Experimental Validation of Selective Histamine H1 Inhibitors

Generative molecular design (GMD) is an increasingly popular strategy for drug discovery, using machine learning models to propose, evaluate and optimize chemical structures against a set of target design criteria. We present the ATOM-GMD platform, a scalable multiprocessing framework to optimize many parameters simultaneously over large populations of proposed molecules. ATOM-GMD uses a junction tree variational autoencoder mapping structures to latent vectors, along with a genetic algorithm operating on latent vector elements, to search a diverse molecular space for compounds that meet the design criteria. We used the ATOM-GMD framework in a lead optimization case study to develop potent and selective histamine H1 receptor antagonists. We synthesized 103 of the top scoring compounds and measured their properties experimentally. Six of the tested compounds bind H1 with Kis between 10 and 100 nM and are at least 100-fold selective relative to muscarinic M2 receptors, validating the effectiveness of our GMD approach.

pharmacology and toxicology↗

bioRxiv2022

Allosteric inhibitors of Zika virus NS2B-NS3 protease targeting protease in super-open conformation

Zika virus (ZIKV) is a member of the Flaviviridae family and is considered a major health threat causing cases of microcephaly in newborns and Guillain-Barre syndrome in adults. Here we targeted a transient deep and hydrophobic pocket of the super-open conformation of ZIKV NS2B-NS3 protease to overcome the limitations of the orthosteric inhibitors. After virtual docking screening of approximately 7 million compounds against the novel allosteric site we selected the top seven candidates and tested them in an enzymatic assay. Six out of seven top candidates selected by the docking screen inhibited ZIKV NS2B-NS3 protease proteolytic activity at low micromolar concentrations, as well as suppressing viral replication. These six compounds, targeting the selected protease pocket conserved in ZIKV as well as several other Flaviviruses, have opened an opportunity for a new kind of drug candidate that might be useful to treat several flaviviral infections.

pharmacology and toxicology↗

bioRxiv2021

Discovery of Potent Triple Inhibitors of Both SARS-CoV-2 Proteases and Human Cathepsin L

There are currently no FDA approved inhibitors of SARS-CoV-2 viral proteases with specific treatment for post-exposure of SARS-CoV-2. Here, we discovered inhibitors containing thiuram disulfide or dithiobis-(thioformate) tested against three key proteases in SARS CoV-2 replication including SARS CoV-2 Main Protease (Mpro), SARS CoV-2 Papain Like Protease (PLpro), and human cathepsin L. The use of thiuram disulfide and dithiobis-(thioformate) covalent inhibitor warheads was inspired by disulfiram, a currently prescribed drug commonly used to treat chronic alcoholism that at the present time is in Phase 2 clinical trials against SARS-CoV-2. At the maximal allowed dose, disulfiram is associated with adverse effects. Our goal was to find more potent inhibitors that target both viral proteases and one essential human protease to reduce the dosage and minimize the adverse effects associated with these agents. We found that compounds coded as RI175, JX 06, and RI172 are the most potent inhibitors from an enzymatic assay against SARS-CoV-2 Mpro, SARS-CoV-2 PLpro, and human cathepsin L with IC50s of 330, 250 nM, and 190 nM about 4.5, 17, and 11.5-fold more potent than disulfiram, respectively. The identified protease inhibitors in this series were also tested against SARS CoV-2 in a cell-based and toxicity assay and were shown to have similar or greater antiviral effect than disulfiram. The identified triple protease inhibitors and their derivatives are promising candidates for treatment of the Covid-19 virus and related variants.

pharmacology and toxicology↗

bioRxiv2021

High-throughput phenotypic screen identifies a new family of potent anti-amoebic compounds

Entamoeba histolytica is a disease-causing parasitic amoeba which affects an estimated 50 million people worldwide, particularly in socioeconomically vulnerable populations experiencing water sanitation issues. Infection with E. histolytica is referred to as amoebiasis, and can cause symptoms such as colitis, dysentery, and even death in extreme cases. Drugs exist that are capable of killing this parasite, but they are hampered by downsides such as significant adverse effects at therapeutic concentrations, issues with patient compliance, the need for additional drugs to kill the transmissible cyst stage, and potential development of resistance. Past screens of small and medium sized chemical libraries have yielded anti-amoebic candidates, thus rendering high-throughput screening a promising direction for new drug discovery in this area. In this study, we screened a curated 80,000-compound library from Janssen pharmaceuticals against E. histolytica trophozoites in vitro, and from it identified a highly potent new inhibitor compound. Further experimentation confirmed the activity of this compound, as well as that of several structurally related compounds, originating from both the Janssen Jump-stARter library, and from chemical vendors, thus highlighting a new structure-activity relationship (SAR). In addition, we confirmed that the compound inhibited E. histolytica survival as rapidly as the current standard of care and inhibited transmissible cysts of the related model organism Entamoeba invadens. Together these results constitute the discovery of a novel class of chemicals with favorable in vitro pharmacological properties which may lead to an improved therapy against this parasite and in all of its life stages. Author summaryThe parasite Entamoeba histolytica represents a significant challenge in the field of global health. It currently infects and causes disease among millions of people worldwide, particularly those lacking access to clean water. Drugs exist to treat this disease, but nevertheless it persists as a problem, likely at least partly due to problems and downsides inherent to these drugs. Hence the search for new and better ones is needed. We report here our contribution to this search, consisting of testing a large, carefully-curated collection of tens of thousands of chemicals for their ability to kill E. histolytica. This large-scale test resulted in the identification of one of the compounds as potently anti-amoebic, capable of killing the parasite cells at extremely low concentrations. Further experimentation found several chemically-related compounds to also possess this property, and additionally found the first compound capable of killing the infective life stage of another Entamoeba parasite. These results have revealed an entire new family of chemicals with good potential for development as better drugs against this disease.

pharmacology and toxicology↗

bioRxiv2021

Crowdsourced Identification of Multi-Target Kinase Inhibitors for RET- and TAU- Based Disease: the Multi-Targeting Drug DREAM Challenge

A continuing challenge in modern medicine is the identification of safer and more efficacious drugs. Precision therapeutics, which have one molecular target, have been long promised to be safer and more effective than traditional therapies. This approach has proven to be challenging for multiple reasons including lack of efficacy, rapidly acquired drug resistance, and narrow patient eligibility criteria. An alternative approach is the development of drugs that address the overall disease network by targeting multiple biological targets ( polypharmacology). Rational development of these molecules will require improved methods for predicting single chemical structures that target multiple drug targets. To address this need, we developed the Multi-Targeting Drug DREAM Challenge, in which we challenged participants to predict single chemical entities that target pro-targets but avoid anti-targets for two unrelated diseases: RET-based tumors and a common form of inherited Tauopathy. Here, we report the results of this DREAM Challenge and the development of two neural network-based machine learning approaches that were applied to the challenge of rational polypharmacology. Together, these platforms provide a potentially useful first step towards developing lead therapeutic compounds that address disease complexity through rational polypharmacology. Author SummaryMany modern drugs are developed with the goal of modulating a single cellular pathway or target. However, many drugs are, in fact, dirty; they target multiple cellular pathways or targets. This phenomenon is known as multi-targeting or polypharmacology. While some strive to develop cleaner therapeutics that eliminate secondary targets, recent work has shown that multi-targeting therapeutics have key advantages for a variety of diseases. However, while multi-targeting drugs that affect a precisely-defined profile of targets may be more effective, it is difficult to computationally predict which molecules have desirable target profiles. Here, we report the results of a competitive crowdsourcing project (the Multi-Targeting Drug DREAM Challenge), where we challenged participants to predict chemicals that have desired target profiles for cancer and neurodegenerative disease.

pharmacology and toxicology↗

bioRxiv2020

Antineoplastic kinase inhibitors: a new class of potent anti-amoebic compounds

Entamoeba histolytica is a protozoan parasite which infects approximately 50 million people worldwide, resulting in an estimated 70,000 deaths every year. Since the 1960s E. histolytica infection has been successfully treated with metronidazole. However, drawbacks to metronidazole therapy exist, including adverse effects, a long treatment course, and the need for an additional drug to prevent cyst-mediated transmission. E. histolytica possesses a kinome with approximately 300 - 400 members, some of which have been previously studied as potential targets for the development of amoebicidal drug candidates. However, while these efforts have uncovered novel potent inhibitors of E. histolytica kinases, none have resulted in approved drugs. In this study we took the alternative approach of testing a set of twelve previously FDA-approved antineoplastic kinase inhibitors against E. histolytica trophozoites in vitro. This resulted in the identification of dasatinib, bosutinib, and ibrutinib as amoebicidal agents at low-micromolar concentrations. Next, we utilized a recently developed computational tool to identify twelve additional drugs with human protein target profiles similar to the three initial hits. Testing of these additional twelve drugs led to the identification of ponatinib, neratinib, and olmutinib were identified as highly potent, with EC50 values in the sub-micromolar range. All of these six drugs were found to kill E. histolytica trophozoites as rapidly as metronidazole. Furthermore, ibrutinib was found to kill the transmissible cyst stage of the model organism E. invadens. Ibrutinib thus possesses both amoebicidal and cysticidal properties, in contrast to all drugs used in the current therapeutic strategy. These findings together reveal antineoplastic kinase inhibitors as a highly promising class of potent drugs against this widespread and devastating disease. Author SummaryEvery year, nearly a hundred thousand people worldwide die from infection by the intestinal parasite Entamoeba histolytica, despite the widespread availability of metronidazole as a treatment. Here we report that six anticancer drugs of the kinase inhibitor class possess potent anti-amoebic properties, with one of them killing both actively dividing parasite and its transmissible cysts. These anticancer kinase inhibitors, including the dual-purpose drug with both amoebicidal and cysticidal activities may be used to treat amoebiasis, especially in cancer patients or in life-threatening brain- and liver-infecting forms of the disease.

microbiology↗

bioRxiv2020

Crosslinking-guided geometry of a complete CXC receptor-chemokine complex and the basis of chemokine subfamily selectivity

Chemokines and their receptors are orchestrators of cell migration in humans. Because dysregulation of the receptor-chemokine system leads to inflammation and cancer, both chemokines and receptors are highly sought therapeutic targets. Yet one of the barriers for their therapeutic targeting is the limited understanding of the structural principles behind receptor-chemokine recognition and selectivity. The existing structures do not include CXC subfamily complexes and lack information about the receptor distal N-termini, despite the importance of the latter in signaling, regulation, and bias. Here we report the discovery of the geometry of the complex between full-length CXCR4, a prototypical CXC receptor and driver of cancer metastasis, and its endogenous ligand CXCL12. By comprehensive disulfide crosslinking, we establish the existence and the structure of a novel interface between the CXCR4 distal N-terminus and CXCL12 {beta}1-strand, while also recapitulating earlier findings from NMR, modeling and crystallography of homologous receptors. A crosslinking-informed high-resolution model of the CXCR4-CXCL12 complex pinpoints the interaction determinants and reveals the occupancy of the receptor major subpocket by the CXCL12 proximal N-terminus. This newly found positioning of the chemokine proximal N-terminus provides a structural explanation of CXC receptor-chemokine selectivity against other subfamilies. Our findings challenge the traditional two-site understanding of receptor-chemokine recognition, suggest the possibility of new affinity and signaling determinants, and fill a critical void on the structural map of an important class of therapeutic targets. These results will aid the rational design of selective chemokine-receptor-targeting small molecules and biologics with novel pharmacology.

biochemistry↗

bioRxiv2019

A receptor for herbivore-associated molecular patterns mediates plant immunity

Plant-herbivore interactions are ubiquitous across nature and drive major agricultural losses. Inducible defense responses triggered through immune recognition aid in host plant protection; however, specific ligand-receptor pairs mediating the initial perception of herbivory remain unknown. Plants in the subtribe Phaseolinae detect herbivore-associated peptides in caterpillar oral secretions and the defined ligands are proteolytic fragments of chloroplastic ATP synthase termed inceptins. Using forward genetic mapping of inceptin-induced responses, we identify a cowpea (Vigna unguiculata) leucine-rich repeat receptor-like protein as an inceptin receptor (INR) sufficient for elicitor-induced responses and enhanced defense against armyworms (Spodoptera exigua). INR defines a receptor by which plants perceive herbivore-associated molecular patterns (HAMPs) and expands the paradigm of surface immune recognition to attack with mandibles.\n\nOne Sentence SummaryA plant cell surface receptor directly perceives peptides associated with caterpillar herbivory.

plant biology↗

bioRxiv2019

Nilotinib, an approved leukemia drug, inhibits Smoothened signaling in Hedgehog-dependent medulloblastoma

Dysregulation of the seven-transmembrane (7TM) receptor Smoothened (SMO) and other components of the Hedgehog (Hh) signaling pathway contributes to the development of cancers including basal cell carcinoma (BCC) and medulloblastoma (MB). However, SMO-specific antagonists produced mixed results in clinical trials, marked by limited efficacy and high rate of acquired resistance in tumors. Here we discovered that Nilotinib, an approved inhibitor of several kinases, possesses an anti-Hh activity, at clinically achievable concentrations, due to direct binding to SMO and inhibition of SMO signaling. Nilotinib was more efficacious than the SMO-specific antagonist Vismodegib in inhibiting growth of two Hh-dependent MB cell lines. It also reduced tumor growth in subcutaneous MB mouse xenograft model. These results indicate that in addition to its known activity against several tyrosine-kinase-mediated proliferative pathways, Nilotinib is a direct inhibitor of the Hh pathway. The newly discovered extension of Nilotinibs target profile holds promise for the treatment of Hh-dependent cancers.

cancer biology↗

bioRxiv2018

Antimalarial drug mefloquine kills both trophozoite and cyst stages of Entamoeba

Entamoeba histolytica is a protozoan parasite which infects approximately 50 million people worldwide, resulting in an estimated 70,000 deaths every year. Since the 1960s E. histolytica infection has been successfully treated with metronidazole. However, drawbacks to metronidazole therapy exist, including adverse effects, length of treatment, and the need for additional drugs to prevent transmission. All of these may decrease patient compliance and hence increase disease severity and spread of infection. In this study we identified the antimalarial drug mefloquine as possessing more potent, rapid, amoebicidal in vitro activity against E. histolytica trophozoites than metronidazole. We also showed that mefloquine could kill the cysts of a closely related reptilian parasite Entamoeba invadens unlike metronidazole. Additionally, mefloquine is known to possess a much longer half-life in human patients than metronidazole. This property, along with mefloquines rapid and broad action against E. histolytica position it as a promising new drug candidate against this widespread and devastating disease.\n\nAuthor SummaryEvery year, around 70,000 people worldwide die from infection by the intestinal parasite Entamoeba histolytica, despite the widespread availability of the drug metronidazole as a treatment. Part of the reason for this may be due to issues with patients failing to comply with the full course of treatment for the drug, due either to unpleasant side-effects, to the somewhat long treatment period, or the need for a secondary drug to kill the transmissible life stage of the parasite. In this report we discovered that the antimalarial drug mefloquine killed E. histolytica more potently and more rapidly than metronidazole, and, importantly, also killed the transmissible cyst stage of another Entamoeba species used as a model system. These findings make mefloquine an excellent candidate for an alternative drug to the current standard, with a simpler course of treatment and a more effective strategy to reduce the spread of this disease.

pharmacology and toxicology↗

bioRxiv2018

Identification and design of vinyl sulfone inhibitors against Cryptopain1, which is a cysteine protease from cryptosporidiosis causingCryptosporidium parvum

Cryptosporidiosis, a disease marked by diarrhea in adults and stunted growth in children, is associated with the unicellular protozoan pathogen Cryptosporidium; often the species parvum. Cryptopain-1, a cysteine protease characterized in the genome of Cryptosporidium parvum, had been earlier shown to be inhibited by a vinyl sulfone compound called K11777 (or K-777). Cysteine proteases have long been established as valid drug targets, which can be covalently and selectively inhibited by vinyl sulfones. This computational study was initiated to identify purchasable vinyl sulfone compounds, which could possibly inhibit cryptopain-1 with higher efficacy than K11777. Docking simulations screened a number of such possibly better inhibitors. The work was furthered to probe the enzymatic pocket of cryptopain-1, through in-silico mutations, to derive a map of receptor-ligand interactions in the docked complexes. The idea was to provide crucial clues to aid the design of inhibitors, which would be able to bind the protease well by making favorable interactions with important residues of the enzyme. The analyses dictated placement of ligands towards the front of the enzymatic cleft, and disfavored interactions deep within. The S1 and S2 subsites of the enzyme preferred to remain occupied by polar ligand subgroups. Reasonably distanced ring systems and polar backbones of ligands were desired across the cleft. Large as well as inflexible subgroups were not tolerated. Double ringed systems such as substituted napthalene, especially in S1, were exceptions though. The S2 subsite, which is typically a specificity determinant in papain (C1) family cysteine proteases such as cathepsin L-like cryptopain-1, can possibly accommodate polar and hydrophobic ligand subgroups alike.

bioinformatics↗

bioRxiv2017

Functional characterization of 3D-protein structures informed by human genetic diversity

Sequence variation data of the human proteome can be used to analyze 3-dimensional (3D) protein structures to derive functional insights. We used genetic variant data from nearly 150,000 individuals to analyze 3D positional conservation in 4,390 protein structures using 481,708 missense and 264,257 synonymous variants. Sixty percent of protein structures harbor at least one intolerant 3D site as defined by significant depletion of observed over expected missense variation. We established an Angstrom-scale distribution of annotated pathogenic missense variants and showed that they accumulate in proximity to the most intolerant 3D sites. Structural intolerance data correlated with experimental functional read-outs in vitro. The 3D structural intolerance analysis revealed characteristic features of ligand binding pockets, orthosteric and allosteric sites. The identification of novel functional 3D sites based on human genetic data helps to validate, rank or predict drug target binding sites in vivo.

genomics↗