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Puhl AC, Lewicki SA, Gao ZG, Pramanik A, Makarov V, Ekins S, Jacobson KA. Machine learning-aided search for ligands of P2Y 6 and other P2Y receptors. Purinergic Signal 2024:10.1007/s11302-024-10003-4. [PMID: 38526670 DOI: 10.1007/s11302-024-10003-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/12/2024] [Indexed: 03/27/2024] Open
Abstract
The P2Y6 receptor, activated by uridine diphosphate (UDP), is a target for antagonists in inflammatory, neurodegenerative, and metabolic disorders, yet few potent and selective antagonists are known to date. This prompted us to use machine learning as a novel approach to aid ligand discovery, with pharmacological evaluation at three P2YR subtypes: initially P2Y6 and subsequently P2Y1 and P2Y14. Relying on extensive published data for P2Y6R agonists, we generated and validated an array of classification machine learning model using the algorithms deep learning (DL), adaboost classifier (ada), Bernoulli NB (bnb), k-nearest neighbors (kNN) classifier, logistic regression (lreg), random forest classifier (rf), support vector classification (SVC), and XGBoost (XGB) classifier models, and the common consensus was applied to molecular selection of 21 diverse structures. Compounds were screened using human P2Y6R-induced functional calcium transients in transfected 1321N1 astrocytoma cells and fluorescent binding inhibition at closely related hP2Y14R expressed in CHO cells. The hit compound ABBV-744, an experimental anticancer drug with a 6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine scaffold, had multifaceted interactions with the P2YR family: hP2Y6R inhibition in a non-surmountable fashion, suggesting that noncompetitive antagonism, and hP2Y1R enhancement, but not hP2Y14R binding inhibition. Other machine learning-selected compounds were either weak (experimental anti-asthmatic drug AZD5423 with a phenyl-1H-indazole scaffold) or inactive in inhibiting the hP2Y6R. Experimental drugs TAK-593 and GSK1070916 (100 µM) inhibited P2Y14R fluorescent binding by 50% and 38%, respectively, and all other compounds by < 20%. Thus, machine learning has led the way toward revealing previously unknown modulators of several P2YR subtypes that have varied effects.
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Affiliation(s)
- Ana C Puhl
- Collaborations Pharmaceuticals, Inc, 840 Main Campus Drive, Lab 3510, Raleigh, NC, 27606, USA
| | - Sarah A Lewicki
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Zhan-Guo Gao
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Asmita Pramanik
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Vadim Makarov
- Research Center of Biotechnology RAS, Leninsky Prospekt 33-2, 119071, Moscow, Russian Federation
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc, 840 Main Campus Drive, Lab 3510, Raleigh, NC, 27606, USA.
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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2
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Ignatyeva O, Gostev V, Taraskina A, Tsvetkova I, Pavlova P, Sulian O, Ageevets V, Likholetova D, Chulkova P, Nikitina E, Matkava L, Terekhov M, Lisovaya D, Kashtanova D, Ivanov M, Kalinogorskaya O, Avdeeva A, Zhirkov A, Goleva O, Zakharenko S, Zhdanov K, Strizheletsky V, Gomon Y, Kruglov A, Ni O, Noskova T, Gorbova I, Cherenkova G, Shlyk I, Afanasyev A, Yudin V, Makarov V, Sidorenko S, Yudin S. General dynamics of the URT microbiome and microbial signs of recovery in COVID-19 patients. Benef Microbes 2024; 15:145-164. [PMID: 38412868 DOI: 10.1163/18762891-bja00004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/01/2024] [Indexed: 02/29/2024]
Abstract
COVID-19 is caused by an airborne virus, SARS-CoV-2. The upper respiratory tract (URT) is, therefore, the first system to endure the attack. Inhabited by an assemblage of microbial communities, a healthy URT wards off the invasion. However, once invaded, it becomes destabilised, which could be crucial to the establishment and progression of the infection. We examined 696 URT samples collected from 285 COVID-19 patients at three time-points throughout their hospital stay and 100 URT samples from 100 healthy controls. We used 16S ribosomal RNA sequencing to evaluate the abundance of various bacterial taxa, α-diversity, and β-diversity of the URT microbiome. Ordinary least squares regression was used to establish associations between the variables, with age, sex, and antibiotics as covariates. The URT microbiome in the COVID-19 patients was distinctively different from that of healthy controls. In COVID-19 patients, the abundance of 16 genera was significantly reduced. A total of 47 genera were specific to patients, whereas only 2 were unique to controls. The URT samples collected at admission differed more from the control than from the samples collected at later stages of treatment. The following four genera originally depleted in the patients grew significantly by the end of treatment: Fusobacterium, Haemophilus, Neisseria, and Stenotrophomonas. Our findings strongly suggest that SARS-CoV-2 caused significant changes in the URT microbiome, including the emergence of numerous atypical taxa. These findings may indicate increased instability of the URT microbiome in COVID-19 patients. In the course of the treatment, the microbial composition of the URT of COVID-19 patients tended toward that of controls. These microbial changes may be interpreted as markers of recovery.
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Affiliation(s)
- O Ignatyeva
- Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Biomedical Agency of Russia, 10/1 Pogodinskaya St., Moscow, 119121, Russian Federation
| | - V Gostev
- Pediatric Research and Clinical Centre for Infectious Diseases, Federal Biomedical Agency of Russia, 9 Professora Popova St., Saint Petersburg, 197022, Russian Federation
- Mechnikov North-Western State Medical University, 41 Kirochnaya St., Saint Petersburg, 191015, Russian Federation
| | - A Taraskina
- Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Biomedical Agency of Russia, 10/1 Pogodinskaya St., Moscow, 119121, Russian Federation
| | - I Tsvetkova
- Pediatric Research and Clinical Centre for Infectious Diseases, Federal Biomedical Agency of Russia, 9 Professora Popova St., Saint Petersburg, 197022, Russian Federation
| | - P Pavlova
- Pediatric Research and Clinical Centre for Infectious Diseases, Federal Biomedical Agency of Russia, 9 Professora Popova St., Saint Petersburg, 197022, Russian Federation
- Saint-Petersburg State University, 7-9 Universitetskaya Naberezhnaya, Saint Petersburg, 199034, Russian Federation
| | - O Sulian
- Pediatric Research and Clinical Centre for Infectious Diseases, Federal Biomedical Agency of Russia, 9 Professora Popova St., Saint Petersburg, 197022, Russian Federation
| | - V Ageevets
- Pediatric Research and Clinical Centre for Infectious Diseases, Federal Biomedical Agency of Russia, 9 Professora Popova St., Saint Petersburg, 197022, Russian Federation
| | - D Likholetova
- Pediatric Research and Clinical Centre for Infectious Diseases, Federal Biomedical Agency of Russia, 9 Professora Popova St., Saint Petersburg, 197022, Russian Federation
| | - P Chulkova
- Pediatric Research and Clinical Centre for Infectious Diseases, Federal Biomedical Agency of Russia, 9 Professora Popova St., Saint Petersburg, 197022, Russian Federation
| | - E Nikitina
- Pediatric Research and Clinical Centre for Infectious Diseases, Federal Biomedical Agency of Russia, 9 Professora Popova St., Saint Petersburg, 197022, Russian Federation
| | - L Matkava
- Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Biomedical Agency of Russia, 10/1 Pogodinskaya St., Moscow, 119121, Russian Federation
| | - M Terekhov
- Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Biomedical Agency of Russia, 10/1 Pogodinskaya St., Moscow, 119121, Russian Federation
| | - D Lisovaya
- Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Biomedical Agency of Russia, 10/1 Pogodinskaya St., Moscow, 119121, Russian Federation
| | - D Kashtanova
- Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Biomedical Agency of Russia, 10/1 Pogodinskaya St., Moscow, 119121, Russian Federation
| | - M Ivanov
- Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Biomedical Agency of Russia, 10/1 Pogodinskaya St., Moscow, 119121, Russian Federation
| | - O Kalinogorskaya
- Pediatric Research and Clinical Centre for Infectious Diseases, Federal Biomedical Agency of Russia, 9 Professora Popova St., Saint Petersburg, 197022, Russian Federation
| | - A Avdeeva
- Pediatric Research and Clinical Centre for Infectious Diseases, Federal Biomedical Agency of Russia, 9 Professora Popova St., Saint Petersburg, 197022, Russian Federation
- Saint-Petersburg State University, 7-9 Universitetskaya Naberezhnaya, Saint Petersburg, 199034, Russian Federation
| | - A Zhirkov
- Pediatric Research and Clinical Centre for Infectious Diseases, Federal Biomedical Agency of Russia, 9 Professora Popova St., Saint Petersburg, 197022, Russian Federation
| | - O Goleva
- Pediatric Research and Clinical Centre for Infectious Diseases, Federal Biomedical Agency of Russia, 9 Professora Popova St., Saint Petersburg, 197022, Russian Federation
| | - S Zakharenko
- Pediatric Research and Clinical Centre for Infectious Diseases, Federal Biomedical Agency of Russia, 9 Professora Popova St., Saint Petersburg, 197022, Russian Federation
| | - K Zhdanov
- Kirov Military Medical Academy, 6 Akademika Lebedeva St., Saint Petersburg, 194044, Russian Federation
| | - V Strizheletsky
- Saint-Petersburg State University, 7-9 Universitetskaya Naberezhnaya, Saint Petersburg, 199034, Russian Federation
| | - Y Gomon
- Pavlov First Saint-Petersburg State Medical University, 6-8 Lva Tolstogo St., Saint Petersburg, 197022, Russian Federation
| | - A Kruglov
- Moscow Multidisciplinary Clinical Centre 'Kommunarka', 8 Sosenskiy Stan, Kommunarka, Moscow, 142770, Russian Federation
| | - O Ni
- Moscow Multidisciplinary Clinical Centre 'Kommunarka', 8 Sosenskiy Stan, Kommunarka, Moscow, 142770, Russian Federation
| | - T Noskova
- Botkin Clinical Hospital of Infectious Diseases, 3 Mirgorodskaya St., Saint Petersburg, 191167, Russian Federation
| | - I Gorbova
- Botkin Clinical Hospital of Infectious Diseases, 3 Mirgorodskaya St., Saint Petersburg, 191167, Russian Federation
| | - G Cherenkova
- Botkin Clinical Hospital of Infectious Diseases, 3 Mirgorodskaya St., Saint Petersburg, 191167, Russian Federation
| | - I Shlyk
- Pavlov First Saint-Petersburg State Medical University, 6-8 Lva Tolstogo St., Saint Petersburg, 197022, Russian Federation
| | - A Afanasyev
- Pavlov First Saint-Petersburg State Medical University, 6-8 Lva Tolstogo St., Saint Petersburg, 197022, Russian Federation
| | - V Yudin
- Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Biomedical Agency of Russia, 10/1 Pogodinskaya St., Moscow, 119121, Russian Federation
| | - V Makarov
- Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Biomedical Agency of Russia, 10/1 Pogodinskaya St., Moscow, 119121, Russian Federation
| | - S Sidorenko
- Pediatric Research and Clinical Centre for Infectious Diseases, Federal Biomedical Agency of Russia, 9 Professora Popova St., Saint Petersburg, 197022, Russian Federation
- Mechnikov North-Western State Medical University, 41 Kirochnaya St., Saint Petersburg, 191015, Russian Federation
| | - S Yudin
- Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Biomedical Agency of Russia, 10/1 Pogodinskaya St., Moscow, 119121, Russian Federation
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Bonacorsi A, Trespidi G, Scoffone VC, Irudal S, Barbieri G, Riabova O, Monakhova N, Makarov V, Buroni S. Characterization of the dispirotripiperazine derivative PDSTP as antibiotic adjuvant and antivirulence compound against Pseudomonas aeruginosa. Front Microbiol 2024; 15:1357708. [PMID: 38435690 PMCID: PMC10904629 DOI: 10.3389/fmicb.2024.1357708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/06/2024] [Indexed: 03/05/2024] Open
Abstract
Pseudomonas aeruginosa is a major human pathogen, able to establish difficult-to-treat infections in immunocompromised and people with cystic fibrosis (CF). The high rate of antibiotic treatment failure is due to its notorious drug resistance, often mediated by the formation of persistent biofilms. Alternative strategies, capable of overcoming P. aeruginosa resistance, include antivirulence compounds which impair bacterial pathogenesis without exerting a strong selective pressure, and the use of antimicrobial adjuvants that can resensitize drug-resistant bacteria to specific antibiotics. In this work, the dispirotripiperazine derivative PDSTP, already studied as antiviral, was characterized for its activity against P. aeruginosa adhesion to epithelial cells, its antibiotic adjuvant ability and its biofilm inhibitory potential. PDSTP was effective in impairing the adhesion of P. aeruginosa to various immortalized cell lines. Moreover, the combination of clinically relevant antibiotics with the compound led to a remarkable enhancement of the antibiotic efficacy towards multidrug-resistant CF clinical strains. PDSTP-ceftazidime combination maintained its efficacy in vivo in a Galleria mellonella infection model. Finally, the compound showed a promising biofilm inhibitory activity at low concentrations when tested both in vitro and using an ex vivo pig lung model. Altogether, these results validate PDSTP as a promising compound, combining the ability to decrease P. aeruginosa virulence by impairing its adhesion and biofilm formation, with the capability to increase antibiotic efficacy against antibiotic resistant strains.
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Affiliation(s)
- Andrea Bonacorsi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Gabriele Trespidi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Viola C. Scoffone
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Samuele Irudal
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Giulia Barbieri
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Olga Riabova
- Research Center of Biotechnology RAS, Moscow, Russia
| | | | - Vadim Makarov
- Research Center of Biotechnology RAS, Moscow, Russia
| | - Silvia Buroni
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
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Tsedilin A, Borets L, Riabova O, Kazakova E, Tafeenko V, Makarov V. Determination of alkaloid-inspired molecule vindeburnol in rabbit plasma by UPLC-HRMS and its application to pharmacokinetic studies and preliminary metabolite identification. J Pharm Biomed Anal 2024; 239:115917. [PMID: 38101239 DOI: 10.1016/j.jpba.2023.115917] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/07/2023] [Accepted: 12/09/2023] [Indexed: 12/17/2023]
Abstract
The eburnamine-vincamine alkaloids exhibit a range of pharmacological activities. There is a limited understanding of the pharmacokinetics and pharmacodynamics of vindeburnol, a synthetic derivative of this chemical class of alkaloids. A fast and reliable UPLC-HRMS method was developed and validated to quantify vindeburnol in Soviet Chinchilla rabbit plasma from pharmacokinetics studies. An ultra-performance liquid chromatography system equipped with a Waters Acquity UPLC HSS T3 column was used for chromatographic separation by gradient elution with 0.1% (v/v) formic acid in water and acetonitrile. An Impact II QqTOF high-resolution mass spectrometer equipped with an Apollo II electrospray ionization source was used for analysis in positive mode; the ions [M+H]+m/z 269.1648 ± 0.003 and m/z 351.2067 ± 0.003 were monitored for vindeburnol and internal standard (vinpocetine), respectively. Preliminary metabolite profiling was also performed, and the pharmacokinetics of the identified metabolites were evaluated. The mean retention times for vindeburnol and vinpocetine were 2.0 and 3.5 min. The UPLC-HRMS method was validated with accuracy and precision within the 15% acceptance limit (8.2% and 11.0%, respectively). The mean extraction recovery value of vindeburnol from rabbit plasma was 77%. Pharmacokinetic evaluation of vindeburnol revealed that the compound is distributed rapidly with a short elimination half-life. Vindeburnol undergoes extensive first-pass metabolism and is metabolized into hydroxyvindeburnol and vindeburnol glucuronide.
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Affiliation(s)
- Andrey Tsedilin
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-1 Leninsky prospect, 119071 Moscow, Russia
| | - Lyudmila Borets
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-1 Leninsky prospect, 119071 Moscow, Russia
| | - Olga Riabova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-1 Leninsky prospect, 119071 Moscow, Russia
| | - Elena Kazakova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-1 Leninsky prospect, 119071 Moscow, Russia
| | - Victor Tafeenko
- Chemistry Department, Lomonosov Moscow State University, 1-3 Leninskie Gory, 119991 Moscow, Russia
| | - Vadim Makarov
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-1 Leninsky prospect, 119071 Moscow, Russia.
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Zubkov E, Riabova O, Zorkina Y, Egorova A, Ushakova V, Lepioshkin A, Novoselova E, Abramova O, Morozova A, Chekhonin V, Makarov V. Antidepressant-like Effect of the Eburnamine-Type Molecule Vindeburnol in Rat and Mouse Models of Ultrasound-Induced Depression. ACS Chem Neurosci 2024; 15:560-571. [PMID: 38216514 DOI: 10.1021/acschemneuro.3c00590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2024] Open
Abstract
Vindeburnol (VIND, RU24722, BC19), a synthetic molecule derived from the eburnamine-vincamine alkaloid group, has many neuropsychopharmacological effects, but its antidepressant-like effects are poorly understood and have only been described in a few patents. To reliably estimate this effect, vindeburnol was studied in a model of long-term variable-frequency ultrasound (US) exposure at 20-45 kHz in male Wistar rats and BALB/c mice. Vindeburnol was administered chronically for 21 days against a background of simultaneous ultrasound exposure at a dose of 20 mg/kg intraperitoneally (IP). Using four behavioral tests, the sucrose preference test (SPT), the social interaction test (SIT), the open field test (OFT), and the forced swimming test (FST), we found that the treatment with the compound diminished depression-like symptoms in mice and rats. The compound restored the ultrasound-related reduced sucrose consumption to control levels and increased social interaction time in mice and rats compared with those in ultrasound-exposed animals. Vindeburnol showed contraversive results of horizontal and vertical activity in both species and generally did not increase locomotor activity. At the same time, the compound showed a specific effect in the FST, significantly reducing the immobility time. Moreover, we found an increase in norepinephrine, dopamine, and its metabolite levels in the brainstem, as well as an increase in dopamine, 3-methoxytyramine, and 3,4-dihydroxyphenylacetic acid levels in the striatum. We also observed a statistically significant increase in tyrosine hydroxylase (TH) levels in the region containing the locus coeruleus (LC). We suggest that using its distinct chemical structure and pharmacological activity as a starting point could boost antidepressant drug discovery.
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Affiliation(s)
- Eugene Zubkov
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, 119071 Moscow, Russia
- V. Serbsky National Medical Research Center for Psychiatry and Narcology, 23 Kropotkinsky Pereulok, 119034 Moscow, Russia
| | - Olga Riabova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, 119071 Moscow, Russia
| | - Yana Zorkina
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, 119071 Moscow, Russia
- V. Serbsky National Medical Research Center for Psychiatry and Narcology, 23 Kropotkinsky Pereulok, 119034 Moscow, Russia
| | - Anna Egorova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, 119071 Moscow, Russia
| | - Valeriya Ushakova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, 119071 Moscow, Russia
- V. Serbsky National Medical Research Center for Psychiatry and Narcology, 23 Kropotkinsky Pereulok, 119034 Moscow, Russia
| | - Alexander Lepioshkin
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, 119071 Moscow, Russia
| | - Elena Novoselova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, 119071 Moscow, Russia
| | - Olga Abramova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, 119071 Moscow, Russia
- V. Serbsky National Medical Research Center for Psychiatry and Narcology, 23 Kropotkinsky Pereulok, 119034 Moscow, Russia
| | - Anna Morozova
- V. Serbsky National Medical Research Center for Psychiatry and Narcology, 23 Kropotkinsky Pereulok, 119034 Moscow, Russia
| | - Vladimir Chekhonin
- V. Serbsky National Medical Research Center for Psychiatry and Narcology, 23 Kropotkinsky Pereulok, 119034 Moscow, Russia
| | - Vadim Makarov
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, 119071 Moscow, Russia
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Richter M, Döring K, Blaas D, Riabova O, Khrenova M, Kazakova E, Egorova A, Makarov V, Schmidtke M. Molecular mechanism of rhinovirus escape from the Pyrazolo[3,4-d]pyrimidine capsid-binding inhibitor OBR-5-340 via mutations distant from the binding pocket: Derivatives that brake resistance. Antiviral Res 2024; 222:105810. [PMID: 38244889 DOI: 10.1016/j.antiviral.2024.105810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/04/2024] [Accepted: 01/14/2024] [Indexed: 01/22/2024]
Abstract
Rhinoviruses (RVs) cause the common cold. Attempts at discovering small molecule inhibitors have mainly concentrated on compounds supplanting the medium chain fatty acids residing in the sixty icosahedral symmetry-related hydrophobic pockets of the viral capsid of the Rhinovirus-A and -B species. High-affinity binding to these pockets stabilizes the capsid against structural changes necessary for the release of the ss(+) RNA genome into the cytosol of the host cell. However, single-point mutations may abolish this binding. RV-B5 is one of several RVs that are naturally resistant against the well-established antiviral agent pleconaril. However, RV-B5 is strongly inhibited by the pyrazolopyrimidine OBR-5-340. Here, we report on isolation and characterization of RV-B5 mutants escaping OBR-5-340 inhibition and show that substitution of amino acid residues not only within the binding pocket but also remote from the binding pocket hamper inhibition. Molecular dynamics network analysis revealed that strong inhibition occurs when an ensemble of several sequence stretches of the capsid proteins enveloping OBR-5-340 move together with OBR-5-340. Mutations abrogating this dynamic, regardless of whether being localized within the binding pocket or distant from it result in escape from inhibition. Pyrazolo [3,4-d]pyrimidine derivatives overcoming OBR-5-340 escape of various RV-B5 mutants were identified. Our work contributes to the understanding of the properties of capsid-binding inhibitors necessary for potent and broad-spectrum inhibition of RVs.
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Affiliation(s)
- Martina Richter
- Jena University Hospital, Department Medical Microbiology, Section Experimental Virology, Hans-Knoell-Str. 2, 07743 Jena, Germany
| | - Kristin Döring
- Jena University Hospital, Department Medical Microbiology, Section Experimental Virology, Hans-Knoell-Str. 2, 07743 Jena, Germany
| | - Dieter Blaas
- Medical University Vienna, Centre of Med. Biochem. Vienna Biocenter, Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria
| | - Olga Riabova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, 119071 Moscow, Russia
| | - Maria Khrenova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, 119071 Moscow, Russia; Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia
| | - Elena Kazakova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, 119071 Moscow, Russia
| | - Anna Egorova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, 119071 Moscow, Russia
| | - Vadim Makarov
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, 119071 Moscow, Russia.
| | - Michaela Schmidtke
- Jena University Hospital, Department Medical Microbiology, Section Experimental Virology, Hans-Knoell-Str. 2, 07743 Jena, Germany.
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Wu X, Wang W, Stelitano G, Riabova O, Wang B, Niu W, Cocorullo M, Shi R, Chiarelli LR, Makarov V, Lu Y, Li C, Qiao C. Benzothiozinone derivatives with anti-tubercular Activity-Further side chain investigation. Eur J Med Chem 2024; 264:115976. [PMID: 38039794 DOI: 10.1016/j.ejmech.2023.115976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/03/2023]
Abstract
A series of novel benzothiozinone (BTZ) derivatives were designed, prepared and evaluated for antituberculosis activity. Specifically, the BTZ pharmacophore is retained and the previous heterocyclic ring linker is replaced by alkynyl or vinyl linker, the resulting compounds displayed about 5-fold improved antimycobacterial activity. We further revealed that the linker attached tail group affects the compound metabolic stability, potency and other drug like properties. This work led to the discovery of two compounds (A1 and A11) with acceptable low MICs and improved metabolic stability. The representative compound A11 demonstrated bactericidal efficacy in an acute TB infection mouse model.
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Affiliation(s)
- Xiaomei Wu
- College of Pharmaceutical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Wenxin Wang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu Province, China
| | - Giovanni Stelitano
- Department of Biology and Biotechnology, University of Pavia, Pavia, 27100, Italy
| | - Olga Riabova
- Research Center of Biotechnology, The Russian Academy of Sciences, Moscow, 119071, Russia
| | - Bin Wang
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Wei Niu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Mario Cocorullo
- Department of Biology and Biotechnology, University of Pavia, Pavia, 27100, Italy
| | - Rui Shi
- College of Pharmaceutical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology, University of Pavia, Pavia, 27100, Italy
| | - Vadim Makarov
- Research Center of Biotechnology, The Russian Academy of Sciences, Moscow, 119071, Russia
| | - Yu Lu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China.
| | - Chuan Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; Zhongshan Institute for Drug Discovery, Zhongshan, 528400, Guangdong Province, China.
| | - Chunhua Qiao
- College of Pharmaceutical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China.
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8
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Kazakova E, Lane TR, Jones T, Puhl AC, Riabova O, Makarov V, Ekins S. 1-Sulfonyl-3-amino-1 H-1,2,4-triazoles as Yellow Fever Virus Inhibitors: Synthesis and Structure-Activity Relationship. ACS Omega 2023; 8:42951-42965. [PMID: 38024733 PMCID: PMC10653066 DOI: 10.1021/acsomega.3c06106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023]
Abstract
Yellow fever virus (YFV) transmitted by infected mosquitoes causes an acute viral disease for which there are no approved small-molecule therapeutics. Our recently developed machine learning models for YFV inhibitors led to the selection of a new pyrazolesulfonamide derivative RCB16003 with acceptable in vitro activity. We report that the N-phenyl-1-(phenylsulfonyl)-1H-1,2,4-triazol-3-amine class, which was recently identified as active non-nucleoside reverse transcriptase inhibitors against HIV-1, can also be repositioned as inhibitors of yellow fever virus replication. As compared to other Flaviviridae or Togaviridae family viruses tested, both compounds RCB16003 and RCB16007 demonstrate selectivity for YFV over related viruses, with only RCB16007 showing some inhibition of the West Nile virus (EC50 7.9 μM, CC50 17 μM, SI 2.2). We also describe the absorption, distribution, metabolism, and excretion (ADME) in vitro and pharmacokinetics (PK) for RCB16007 in mice. This compound had previously been shown to not inhibit hERG, and we now describe that it has good metabolic stability in mouse and human liver microsomes, low levels of CYP inhibition, high protein binding, and no indication of efflux in Caco-2 cells. A single-dose oral PK study in mice has a T1/2 of 3.4 h and Cmax of 1190 ng/mL, suggesting good availability and stability. We now propose that the N-phenyl-1-(phenylsulfonyl)-1H-1,2,4-triazol-3-amine class may be prioritized for in vivo efficacy testing against YFV.
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Affiliation(s)
- Elena Kazakova
- Federal
Research Centre “Fundamentals of Biotechnology” of the
Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, 119071 Moscow, Russia
| | - Thomas R. Lane
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Thane Jones
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Ana C. Puhl
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Olga Riabova
- Federal
Research Centre “Fundamentals of Biotechnology” of the
Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, 119071 Moscow, Russia
| | - Vadim Makarov
- Federal
Research Centre “Fundamentals of Biotechnology” of the
Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, 119071 Moscow, Russia
| | - Sean Ekins
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
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9
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Jones T, Monakhova N, Guivel-Benhassine F, Lepioshkin A, Bruel T, Lane TR, Schwartz O, Puhl AC, Makarov V, Ekins S. Synthesis and Evaluation of 9-Aminoacridines with SARS-CoV-2 Antiviral Activity. ACS Omega 2023; 8:40817-40822. [PMID: 37929131 PMCID: PMC10620940 DOI: 10.1021/acsomega.3c05900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/04/2023] [Indexed: 11/07/2023]
Abstract
There have been relatively few small molecules developed with direct activity against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Two existing antimalarial drugs, pyronaridine and quinacrine, display whole cell activity against SARS-CoV-2 in A549 + ACE2 cells (pretreatment, IC50 = 0.23 and 0.19 μM, respectively) with moderate cytotoxicity (CC50 = 11.53 and 9.24 μM, respectively). Moreover, pyronaridine displays in vitro activity against SARS-CoV-2 PLpro (IC50 = 1.8 μM). Given their existing antiviral activity, these compounds are strong candidates for repurposing against COVID-19 and prompt us to study the structure-activity relationship of the 9-aminoacridine scaffold against SARS-CoV-2 using traditional medicinal chemistry to identify promising new analogs. Our studies identified several novel analogs possessing potent in vitro activity in U2-OS ACE2 GFP 1-10 and 1-11 (IC50 < 1.0 μM) as well as moderate cytotoxicity (CC50 > 4.0 μM). Compounds such as 7g, 9c, and 7e were more active, demonstrating selectivity indices SI > 10, and 9c displayed the strongest activity (IC50 ≤ 0.42 μM, CC50 ≥ 4.41 μM, SI > 10) among them, indicating that it has potential as a new lead molecule in this series against COVID-19.
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Affiliation(s)
- Thane Jones
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Natalia Monakhova
- Federal
Research Centre “Fundamentals of Biotechnology” of the
Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, Moscow 119071, Russia
| | | | - Alexander Lepioshkin
- Federal
Research Centre “Fundamentals of Biotechnology” of the
Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, Moscow 119071, Russia
| | - Timothée Bruel
- Institut
Pasteur, 28 rue du Dr Roux, Paris Cedex 15 75724, France
| | - Thomas R. Lane
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Olivier Schwartz
- Institut
Pasteur, 28 rue du Dr Roux, Paris Cedex 15 75724, France
| | - Ana C. Puhl
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Vadim Makarov
- Federal
Research Centre “Fundamentals of Biotechnology” of the
Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, Moscow 119071, Russia
| | - Sean Ekins
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
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10
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Jones T, Tavis JE, Li Q, Riabova O, Monakhova N, Bradley DP, Lane TR, Makarov V, Ekins S. Antiviral Evaluation of Dispirotripiperazines against Hepatitis B Virus. J Med Chem 2023; 66:12459-12467. [PMID: 37611244 PMCID: PMC11017374 DOI: 10.1021/acs.jmedchem.3c00974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Hepatitis B virus (HBV) is a hepatotropic DNA virus that replicates by reverse transcription. It chronically infects >296 million people worldwide, including ∼850,000 in the USA, and kills 820,000 annually worldwide. Current nucleos(t)ide analogue (NA) or pegylated interferon α therapies do not eradicate the virus and would benefit from a complementary antiviral drug. We performed a preliminary screen of 28 dispirotripiperazines against HBV, identifying 9 hits with EC50 of 0.7-25 μM. Compound 11826096 displays the most potent activity and represents a promising lead for future optimization. While the mechanism of action is unknown, preliminary assays limit possible targets to activities involved in RNA accumulation, translation, capsid assembly, and/or capsid stability. In addition, we built machine learning models to determine if they were able to predict the activity of this series of compounds. The novelty of these molecules indicated they were outside of the applicability domain of these models.
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Affiliation(s)
- Thane Jones
- Collaborations Pharmaceuticals Inc., 840 Main Campus Dr., Lab 3510, Raleigh, NC, USA
| | - John E. Tavis
- Saint Louis University School of Medicine, 1100 S. Grand Blvd., St. Louis, MO, USA
| | - Qilan Li
- Saint Louis University School of Medicine, 1100 S. Grand Blvd., St. Louis, MO, USA
| | - Olga Riabova
- Research Center of Biotechnology RAS, Leninsky Prospekt 33-2, 119071, Moscow, Russia
| | - Natalia Monakhova
- Research Center of Biotechnology RAS, Leninsky Prospekt 33-2, 119071, Moscow, Russia
| | - Daniel P. Bradley
- Saint Louis University School of Medicine, 1100 S. Grand Blvd., St. Louis, MO, USA
| | - Thomas R. Lane
- Collaborations Pharmaceuticals Inc., 840 Main Campus Dr., Lab 3510, Raleigh, NC, USA
| | - Vadim Makarov
- Research Center of Biotechnology RAS, Leninsky Prospekt 33-2, 119071, Moscow, Russia
| | - Sean Ekins
- Collaborations Pharmaceuticals Inc., 840 Main Campus Dr., Lab 3510, Raleigh, NC, USA
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11
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Lane TR, Fu J, Sherry B, Tarbet B, Hurst BL, Riabova O, Kazakova E, Egorova A, Clarke P, Leser JS, Frost J, Rudy M, Tyler KL, Klose T, Volobueva AS, Belyaevskaya SV, Zarubaev VV, Kuhn RJ, Makarov V, Ekins S. Efficacy of an isoxazole-3-carboxamide analog of pleconaril in mouse models of Enterovirus-D68 and Coxsackie B5. Antiviral Res 2023; 216:105654. [PMID: 37327878 PMCID: PMC10527014 DOI: 10.1016/j.antiviral.2023.105654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/05/2023] [Accepted: 06/13/2023] [Indexed: 06/18/2023]
Abstract
Enteroviruses (EV) cause a number of life-threatening infectious diseases. EV-D68 is known to cause respiratory illness in children that can lead to acute flaccid myelitis. Coxsackievirus B5 (CVB5) is commonly associated with hand-foot-mouth disease. There is no antiviral treatment available for either. We have developed an isoxazole-3-carboxamide analog of pleconaril (11526092) which displayed potent inhibition of EV-D68 (IC50 58 nM) as well as other enteroviruses including the pleconaril-resistant Coxsackievirus B3-Woodruff (IC50 6-20 nM) and CVB5 (EC50 1 nM). Cryo-electron microscopy structures of EV-D68 in complex with 11526092 and pleconaril demonstrate destabilization of the EV-D68 MO strain VP1 loop, and a strain-dependent effect. A mouse respiratory model of EV-D68 infection, showed 3-log decreased viremia, favorable cytokine response, as well as statistically significant 1-log reduction in lung titer reduction at day 5 after treatment with 11526092. An acute flaccid myelitis neurological infection model did not show efficacy. 11526092 was tested in a mouse model of CVB5 infection and showed a 4-log TCID50 reduction in the pancreas. In summary, 11526092 represents a potent in vitro inhibitor of EV with in vivo efficacy in EV-D68 and CVB5 animal models suggesting it is worthy of further evaluation as a potential broad-spectrum antiviral therapeutic against EV.
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Affiliation(s)
- Thomas R Lane
- Collaborations Pharmaceuticals Inc., Raleigh, NC, USA
| | - Jianing Fu
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Barbara Sherry
- Department of Molecular Biomedical Sciences, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA
| | - Bart Tarbet
- Institute for Antiviral Research, Utah State University, Logan, UT, USA; Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA
| | - Brett L Hurst
- Institute for Antiviral Research, Utah State University, Logan, UT, USA; Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA
| | - Olga Riabova
- Research Center of Biotechnology RAS, 33-1 Leninsky prospect, 119071, Moscow, Russia
| | - Elena Kazakova
- Research Center of Biotechnology RAS, 33-1 Leninsky prospect, 119071, Moscow, Russia
| | - Anna Egorova
- Research Center of Biotechnology RAS, 33-1 Leninsky prospect, 119071, Moscow, Russia
| | - Penny Clarke
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - J Smith Leser
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Joshua Frost
- Department of Immunology and Microbiology, Infectious Disease, Medicine and Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Kenneth L Tyler
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Department of Veterans Affairs, Aurora, CO, USA
| | - Thomas Klose
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | | | | | - Vladimir V Zarubaev
- Saint Petersburg Pasteur Institute, 14 Mira Street, 197101, Saint Petersburg, Russia
| | - Richard J Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Vadim Makarov
- Research Center of Biotechnology RAS, 33-1 Leninsky prospect, 119071, Moscow, Russia
| | - Sean Ekins
- Collaborations Pharmaceuticals Inc., Raleigh, NC, USA.
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12
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Degiacomi G, Gianibbi B, Recchia D, Stelitano G, Truglio GI, Marra P, Stamilla A, Makarov V, Chiarelli LR, Manetti F, Pasca MR. CanB, a Druggable Cellular Target in Mycobacterium tuberculosis. ACS Omega 2023; 8:25209-25220. [PMID: 37483251 PMCID: PMC10357428 DOI: 10.1021/acsomega.3c02311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/05/2023] [Indexed: 07/25/2023]
Abstract
Treatment against tuberculosis can lead to the selection of drug-resistant Mycobacterium tuberculosis strains. To tackle this serious threat, new targets from M. tuberculosis are needed to develop novel effective drugs. In this work, we aimed to provide a possible workflow to validate new targets and inhibitors by combining genetic, in silico, and enzymological approaches. CanB is one of the three M. tuberculosis β-carbonic anhydrases that catalyze the reversible reaction of CO2 hydration to form HCO3- and H+. To this end, we precisely demonstrated that CanB is essential for the survival of the pathogen in vitro by constructing conditional mutants. In addition, to search for CanB inhibitors, conditional canB mutants were also constructed using the Pip-ON system. By molecular docking and minimum inhibitory concentration assays, we selected three molecules that inhibit the growth in vitro of M. tuberculosis wild-type strain and canB conditional mutants, thus implementing a target-to-drug approach. The lead compound also showed a bactericidal activity by the time-killing assay. We further studied the interactions of these molecules with CanB using enzymatic assays and differential scanning fluorimetry thermal shift analysis. In conclusion, the compounds identified by the in silico screening proved to have a high affinity as CanB ligands endowed with antitubercular activity.
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Affiliation(s)
- Giulia Degiacomi
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
| | - Beatrice Gianibbi
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena 53100, Italy
| | - Deborah Recchia
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
| | - Giovanni Stelitano
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
| | | | - Paola Marra
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
| | - Alessandro Stamilla
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
| | - Vadim Makarov
- Bakh
Institute of Biochemistry, Russian Academy
of Science, Moscow 119071, Russia
| | - Laurent Robert Chiarelli
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
| | - Fabrizio Manetti
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena 53100, Italy
| | - Maria Rosalia Pasca
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
- Fondazione
IRCCS Policlinico San Matteo, Pavia 27100, Italy
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13
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Fan D, Wang B, Stelitano G, Savková K, Riabova O, Shi R, Wu X, Chiarelli LR, Mikušová K, Makarov V, Lu Y, Hong Y, Qiao C. Side Chain-Modified Benzothiazinone Derivatives with Anti-Mycobacterial Activity. Biomedicines 2023; 11:1975. [PMID: 37509615 PMCID: PMC10377601 DOI: 10.3390/biomedicines11071975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/03/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Tuberculosis (TB) is a leading infectious disease with serious antibiotic resistance. The benzothiazinone (BTZ) scaffold PBTZ169 kills Mycobacterium tuberculosis (Mtb) through the inhibition of the essential cell wall enzyme decaprenylphosphoryl-β-D-ribose 2'-oxidase (DprE1). PBTZ169 shows anti-TB potential in animal models and pilot clinical tests. Although highly potent, the BTZ type DprE1 inhibitors in general show extremely low aqueous solubility, which adversely affects the drug-like properties. To improve the compounds physicochemical properties, we generated a series of BTZ analogues. Several optimized compounds had MIC values against Mtb lower than 0.01 µM. The representative compound 37 displays improved solubility and bioavailability compared to the lead compound. Additionally, compound 37 shows Mtb-killing ability in an acute infection mouse model.
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Affiliation(s)
- Dongguang Fan
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Bin Wang
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research, Beijing Chest Hospital, Beijing 101149, China
| | - Giovanni Stelitano
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Karin Savková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 84215 Bratislava, Slovakia
| | - Olga Riabova
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Rui Shi
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Xiaomei Wu
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Katarína Mikušová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 84215 Bratislava, Slovakia
| | - Vadim Makarov
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Yu Lu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research, Beijing Chest Hospital, Beijing 101149, China
| | - Yuzhi Hong
- Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, China
- Suzhou Key Laboratory of Pathogen Bioscience and Anti-Infective Medicine, Suzhou Medical College, Soochow University, Suzhou 215123, China
| | - Chunhua Qiao
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
- Suzhou Key Laboratory of Pathogen Bioscience and Anti-Infective Medicine, Suzhou Medical College, Soochow University, Suzhou 215123, China
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14
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Egorova A, Richter M, Khrenova M, Dietrich E, Tsedilin A, Kazakova E, Lepioshkin A, Jahn B, Chernyshev V, Schmidtke M, Makarov V. Pyrrolo[2,3- e]indazole as a novel chemotype for both influenza A virus and pneumococcal neuraminidase inhibitors. RSC Adv 2023; 13:18253-18261. [PMID: 37350858 PMCID: PMC10282731 DOI: 10.1039/d3ra02895j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/12/2023] [Indexed: 06/24/2023] Open
Abstract
Influenza infections are often exacerbated by secondary bacterial infections, primarily caused by Streptococcus pneumoniae. Both respiratory pathogens have neuraminidases that support infection. Therefore, we hypothesized that dual inhibitors of viral and bacterial neuraminidases might be an advantageous strategy for treating seasonal and pandemic influenza pneumonia complicated by bacterial infections. By screening our in-house chemical library, we discovered a new chemotype that may be of interest for a further campaign to find small molecules against influenza. Our exploration of the pyrrolo[2,3-e]indazole space led to the identification of two hit compounds, 6h and 12. These molecules were well-tolerated by MDCK cells and inhibited the replication of H3N2 and H1N1 influenza A virus strains. Moreover, both compounds suppress viral and pneumococcal neuraminidases indicating their dual activity. Given its antiviral activity, pyrrolo[2,3-e]indazole has been identified as a promising scaffold for the development of novel neuraminidase inhibitors that are active against influenza A virus and S. pneumoniae.
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Affiliation(s)
- Anna Egorova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS) 33-2 Leninsky Prospect 119071 Moscow Russia
| | - Martina Richter
- Department of Medical Microbiology, Section of Experimental Virology, Jena University Hospital Hans-Knöll-Straße 2 07745 Jena Germany
| | - Maria Khrenova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS) 33-2 Leninsky Prospect 119071 Moscow Russia
- Chemistry Department, Lomonosov Moscow State University 1-3 Leninskie Gory 119991 Moscow Russia
| | - Elisabeth Dietrich
- Department of Medical Microbiology, Section of Experimental Virology, Jena University Hospital Hans-Knöll-Straße 2 07745 Jena Germany
| | - Andrey Tsedilin
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS) 33-2 Leninsky Prospect 119071 Moscow Russia
| | - Elena Kazakova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS) 33-2 Leninsky Prospect 119071 Moscow Russia
| | - Alexander Lepioshkin
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS) 33-2 Leninsky Prospect 119071 Moscow Russia
| | - Birgit Jahn
- Department of Medical Microbiology, Section of Experimental Virology, Jena University Hospital Hans-Knöll-Straße 2 07745 Jena Germany
| | - Vladimir Chernyshev
- Chemistry Department, Lomonosov Moscow State University 1-3 Leninskie Gory 119991 Moscow Russia
- Frumkin Institute of Physical Chemistry and Electrochemistry of the Russian Academy of Sciences 31-4 Leninsky Prospect 119071 Moscow Russia
| | - Michaela Schmidtke
- Department of Medical Microbiology, Section of Experimental Virology, Jena University Hospital Hans-Knöll-Straße 2 07745 Jena Germany
| | - Vadim Makarov
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS) 33-2 Leninsky Prospect 119071 Moscow Russia
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15
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Lane T, Makarov V, Nelson JAE, Meeker RB, Sanna G, Riabova O, Kazakova E, Monakhova N, Tsedilin A, Urbina F, Jones T, Suchy A, Ekins S. N-Phenyl-1-(phenylsulfonyl)-1 H-1,2,4-triazol-3-amine as a New Class of HIV-1 Non-nucleoside Reverse Transcriptase Inhibitor. J Med Chem 2023; 66:6193-6217. [PMID: 37130343 PMCID: PMC10269403 DOI: 10.1021/acs.jmedchem.2c02055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Highly active antiretroviral therapy (HAART) has revolutionized human immunodeficiency virus (HIV) healthcare, turning it from a terminal to a potentially chronic disease, although some patients can develop severe comorbidities. These include neurological complications, such as HIV-associated neurocognitive disorders (HAND), which result in cognitive and/or motor function symptoms. We now describe the discovery, synthesis, and evaluation of a new class of N-phenyl-1-(phenylsulfonyl)-1H-1,2,4-triazol-3-amine HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTI) aimed at avoiding HAND. The most promising molecule, 12126065, exhibited antiviral activity against wild-type HIV-1 in TZM cells (EC50 = 0.24 nM) with low in vitro cytotoxicity (CC50 = 4.8 μM) as well as retained activity against clinically relevant HIV mutants. 12126065 also demonstrated no in vivo acute or subacute toxicity, good in vivo brain penetration, and minimal neurotoxicity in mouse neurons up to 10 μM, with a 50% toxicity concentration (TC50) of >100 μM, well below its EC50.
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Affiliation(s)
- Thomas Lane
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab, 3510, Raleigh, NC 27606, USA
| | - Vadim Makarov
- Research Center of Biotechnology RAS, Leninsky Prospekt 33-2, 119071, Moscow 119071, Russia
| | - Julie A. E. Nelson
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Rick B. Meeker
- Department of Neurology, University of North Carolina, NC 27514, USA
| | - Giuseppina Sanna
- Department of Biomedical Science, University of Cagliari, Monserrato, 09042, Italy
| | - Olga Riabova
- Research Center of Biotechnology RAS, Leninsky Prospekt 33-2, 119071, Moscow 119071, Russia
| | - Elena Kazakova
- Research Center of Biotechnology RAS, Leninsky Prospekt 33-2, 119071, Moscow 119071, Russia
| | - Natalia Monakhova
- Research Center of Biotechnology RAS, Leninsky Prospekt 33-2, 119071, Moscow 119071, Russia
| | - Andrey Tsedilin
- Research Center of Biotechnology RAS, Leninsky Prospekt 33-2, 119071, Moscow 119071, Russia
| | - Fabio Urbina
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab, 3510, Raleigh, NC 27606, USA
| | - Thane Jones
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab, 3510, Raleigh, NC 27606, USA
| | - Ashley Suchy
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Sean Ekins
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab, 3510, Raleigh, NC 27606, USA
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16
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Koryakova A, Shcherbakova V, Riabova O, Kazaishvili Y, Bolgarin R, Makarov V. Antituberculosis Macozinone Extended-Release Tablets To Enhance Bioavailability: a Pilot Pharmacokinetic Study in Beagle Dogs. Microbiol Spectr 2023; 11:e0232722. [PMID: 36507624 PMCID: PMC9927148 DOI: 10.1128/spectrum.02327-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/14/2022] [Indexed: 12/14/2022] Open
Abstract
Macozinone (MCZ; PBTZ169) is a first-in-class antituberculosis clinical-stage benzothiazinone-based drug candidate. Although its efficacy and safety have been strongly proven in several preclinical and clinical studies, the physicochemical and pharmacokinetic properties specific to MCZ required further optimization. Accordingly, this study aimed to evaluate the pharmacokinetics of MCZ administered as extended-release (ER) tablets F2 and F6 compared to immediate-release (IR) dispersible tablets for oral suspension. Oral absorption of MCZ from ER tablets was significantly different from that of IR tablets after a single oral dose in Beagle dogs in both fasted and fed states. In addition, food directly affects the bioavailability of MCZ from ER tablets but does not affect it from IR tablets. The high values of relative bioavailability of the prolonged-release tablets F2 and F6 compared to the IR tablets may indicate an indirect confirmation of their gastroretentive properties. Taken together, pharmacokinetic parameters have demonstrated that these MCZ oral formulations not just enhance drug bioavailability but may also improve regimen adherence by reducing MCZ dose frequency and reducing the development of drug resistance. IMPORTANCE Macozinone (MCZ) is the newest first-in-class clinical-stage benzothiazinone-based drug candidate for the treatment of tuberculosis. Yet, the extremely low oral bioavailability of MCZ, a major problem in clinical trials, needed to be addressed, and we are pleased to present our attempts to solve this issue. We report that extended-release tablets of MCZ significantly increased key pharmacokinetic parameters in the preclinical setting. We suggest that these MCZ oral formulations not just enhance drug bioavailability but may also improve regimen adherence by reducing MCZ dose frequency and reducing the development of drug resistance.
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Affiliation(s)
| | | | - Olga Riabova
- Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), Moscow, Russia
| | | | | | - Vadim Makarov
- Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), Moscow, Russia
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17
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Desfontaine V, Guinchard S, Marques S, Vocat A, Moulfi F, Versace F, Huser-Pitteloud J, Ivanyuk A, Bardinet C, Makarov V, Ryabova O, André P, Prod'Hom S, Chtioui H, Buclin T, Cole ST, Decosterd L. Optimized LC-MS/MS quantification of tuberculosis drug candidate macozinone (PBTZ169), its dearomatized Meisenheimer Complex and other metabolites, in human plasma and urine. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1215:123555. [PMID: 36563654 PMCID: PMC9883661 DOI: 10.1016/j.jchromb.2022.123555] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022]
Abstract
Tuberculosis, and especially multidrug-resistant tuberculosis (MDR-TB), is a major global health threat which emphasizes the need to develop new agents to improve and shorten treatment of this difficult-to-manage infectious disease. Among the new agents, macozinone (PBTZ169) is one of the most promising candidates, showing extraordinary potency in vitro and in murine models against drug-susceptible and drug-resistant Mycobacterium tuberculosis. A previous analytical method using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) was developed by our group to support phase I clinical trials of PBTZ169. These plasma sample analyses revealed the presence of several additional metabolites among which the most prominent was H2PBTZ, a reduced species obtained by dearomatization of macozinone, one of the first examples of Meisenheimer Complex (MC) metabolites identified in mammals. Identification of these new metabolites required the optimization of our original method for enhancing the selectivity between isobaric metabolites as well as for ensuring optimal stability for H2PBTZ analyses. Sample preparation methods were also developed for plasma and urine, followed by extensive quantitative validation in accordance with international bioanalytical method recommendations, which include selectivity, linearity, qualitative and quantitative matrix effect, trueness, precision and the establishment of accuracy profiles using β-expectation tolerance intervals for known and newer analytes. The newly optimized methods have been applied in a subsequent Phase Ib clinical trial conducted in our University Hospital with healthy subjects. H2PBTZ was found to be the most abundant species circulating in plasma, underscoring the importance of measuring accurately and precisely this unprecedented metabolite. Low concentrations were found in urine for all monitored analytes, suggesting extensive metabolism before renal excretion.
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Affiliation(s)
- Vincent Desfontaine
- Laboratory & Service of Clinical Pharmacology, Department of Laboratory Medicine and Pathology, University Hospital of Lausanne and University of Lausanne, Switzerland
| | - Sylvie Guinchard
- Laboratory & Service of Clinical Pharmacology, Department of Laboratory Medicine and Pathology, University Hospital of Lausanne and University of Lausanne, Switzerland
| | - Sara Marques
- Laboratory & Service of Clinical Pharmacology, Department of Laboratory Medicine and Pathology, University Hospital of Lausanne and University of Lausanne, Switzerland
| | - Anthony Vocat
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Farizade Moulfi
- Innovative Medicines for Tuberculosis (IM4TB), Lausanne, Switzerland
| | - François Versace
- Laboratory & Service of Clinical Pharmacology, Department of Laboratory Medicine and Pathology, University Hospital of Lausanne and University of Lausanne, Switzerland
| | - Jeff Huser-Pitteloud
- Laboratory & Service of Clinical Pharmacology, Department of Laboratory Medicine and Pathology, University Hospital of Lausanne and University of Lausanne, Switzerland
| | - Anton Ivanyuk
- Laboratory & Service of Clinical Pharmacology, Department of Laboratory Medicine and Pathology, University Hospital of Lausanne and University of Lausanne, Switzerland
| | - Carine Bardinet
- Laboratory & Service of Clinical Pharmacology, Department of Laboratory Medicine and Pathology, University Hospital of Lausanne and University of Lausanne, Switzerland
| | - Vadim Makarov
- Innovative Medicines for Tuberculosis (IM4TB), Lausanne, Switzerland,Federal Research Center “Fundamentals of Biotechnology RAS”, Moscow, Russia
| | - Olga Ryabova
- Federal Research Center “Fundamentals of Biotechnology RAS”, Moscow, Russia
| | - Pascal André
- Laboratory & Service of Clinical Pharmacology, Department of Laboratory Medicine and Pathology, University Hospital of Lausanne and University of Lausanne, Switzerland
| | - Sylvain Prod'Hom
- Laboratory & Service of Clinical Pharmacology, Department of Laboratory Medicine and Pathology, University Hospital of Lausanne and University of Lausanne, Switzerland
| | - Haithem Chtioui
- Laboratory & Service of Clinical Pharmacology, Department of Laboratory Medicine and Pathology, University Hospital of Lausanne and University of Lausanne, Switzerland
| | - Thierry Buclin
- Laboratory & Service of Clinical Pharmacology, Department of Laboratory Medicine and Pathology, University Hospital of Lausanne and University of Lausanne, Switzerland,Innovative Medicines for Tuberculosis (IM4TB), Lausanne, Switzerland
| | - Stewart T. Cole
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland,Innovative Medicines for Tuberculosis (IM4TB), Lausanne, Switzerland
| | - Laurent Decosterd
- Laboratory & Service of Clinical Pharmacology, Department of Laboratory Medicine and Pathology, University Hospital of Lausanne and University of Lausanne, Switzerland,Corresponding author.
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18
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Degiacomi G, Makarov V, Pasca MR, Chiarelli LR. New Drugs and Novel Cellular Targets against Tuberculosis. Int J Mol Sci 2022; 23:ijms232213680. [PMID: 36430162 PMCID: PMC9693588 DOI: 10.3390/ijms232213680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/07/2022] [Indexed: 11/10/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the etiological agent of tuberculosis (TB), one of the most life-threatening communicable diseases, which causes 10 million new cases each year and results in an estimated 1 [...].
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Affiliation(s)
- Giulia Degiacomi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Vadim Makarov
- Research Center of Biotechnology RAS, 119071 Moscow, Russia
| | - Maria Rosalia Pasca
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Laurent Roberto Chiarelli
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
- Correspondence:
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19
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Scoffone VC, Irudal S, AbuAlshaar A, Piazza A, Trespidi G, Barbieri G, Makarov V, Migliavacca R, De Rossi E, Buroni S. Bactericidal and Anti-Biofilm Activity of the FtsZ Inhibitor C109 against Acinetobacter baumannii. Antibiotics (Basel) 2022; 11:1571. [PMID: 36358226 PMCID: PMC9687021 DOI: 10.3390/antibiotics11111571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/03/2022] [Accepted: 11/05/2022] [Indexed: 09/29/2023] Open
Abstract
In the last few years, Acinetobacter baumannii has ranked as a number one priority due to its Multi Drug Resistant phenotype. The different metabolic states, such as the one adopted when growing as biofilm, help the bacterium to resist a wide variety of compounds, placing the discovery of new molecules able to counteract this pathogen as a topic of utmost importance. In this context, bacterial cell division machinery and the conserved protein FtsZ are considered very interesting cellular targets. The benzothiadiazole compound C109 is able to inhibit bacterial growth and to block FtsZ GTPase and polymerization activities in Burkholderia cenocepacia, Pseudomonas aeruginosa, and Staphylococcus aureus. In this work, the activity of C109 was tested against a panel of antibiotic sensitive and resistant A. baumannii strains. Its ability to inhibit biofilm formation was explored, together with its activity against the A. baumannii FtsZ purified protein. Our results indicated that C109 has good MIC values against A. baumannii clinical isolates. Moreover, its antibiofilm activity makes it an interesting alternative treatment, effective against diverse metabolic states. Finally, its activity was confirmed against A. baumannii FtsZ.
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Affiliation(s)
- Viola Camilla Scoffone
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Samuele Irudal
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Aseel AbuAlshaar
- Unit of Microbiology and Clinical Microbiology, Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, University of Pavia, 27100 Pavia, Italy
| | - Aurora Piazza
- Unit of Microbiology and Clinical Microbiology, Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, University of Pavia, 27100 Pavia, Italy
| | - Gabriele Trespidi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Giulia Barbieri
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Vadim Makarov
- Research Center of Biotechnology RAS, 119071 Moscow, Russia
| | - Roberta Migliavacca
- Unit of Microbiology and Clinical Microbiology, Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, University of Pavia, 27100 Pavia, Italy
| | - Edda De Rossi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Silvia Buroni
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
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20
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Rank L, Puhl AC, Havener TM, Anderson E, Foil DH, Zorn KM, Monakhova N, Riabova O, Hickey AJ, Makarov V, Ekins S. Multiple approaches to repurposing drugs for neuroblastoma. Bioorg Med Chem 2022; 73:117043. [PMID: 36208544 PMCID: PMC9870653 DOI: 10.1016/j.bmc.2022.117043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 01/26/2023]
Abstract
Neuroblastoma (NB) is the second leading extracranial solid tumor of early childhood with about two-thirds of cases presenting before the age of 5, and accounts for roughly 15 percent of all pediatric cancer fatalities in the United States. Treatments against NB are lacking, resulting in a low survival rate in high-risk patients. A repurposing approach using already approved or clinical stage compounds can be used for diseases for which the patient population is small, and the commercial market limited. We have used Bayesian machine learning, in vitro cell assays, and combination analysis to identify molecules with potential use for NB. We demonstrated that pyronaridine (SH-SY5Y IC50 1.70 µM, SK-N-AS IC50 3.45 µM), BAY 11-7082 (SH-SY5Y IC50 0.85 µM, SK-N-AS IC50 1.23 µM), niclosamide (SH-SY5Y IC50 0.87 µM, SK-N-AS IC50 2.33 µM) and fingolimod (SH-SY5Y IC50 4.71 µM, SK-N-AS IC50 6.11 µM) showed cytotoxicity against NB. As several of the molecules are approved drugs in the US or elsewhere, they may be repurposed more readily for NB treatment. Pyronaridine was also tested in combinations in SH-SY5Y cells and demonstrated an antagonistic effect with either etoposide or crizotinib. Whereas when crizotinib and etoposide were combined with each other they had a synergistic effect in these cells. We have also described several analogs of pyronaridine to explore the structure-activity relationship against cell lines. We describe multiple molecules demonstrating cytotoxicity against NB and the further evaluation of these molecules and combinations using other NB cells lines and in vivo models will be important in the future to assess translational potential.
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Affiliation(s)
- Laura Rank
- Collaborations Pharmaceuticals, Inc, 840 Main Campus Drive, Lab 3510, Raleigh, NC, USA
| | - Ana C Puhl
- Collaborations Pharmaceuticals, Inc, 840 Main Campus Drive, Lab 3510, Raleigh, NC, USA.
| | - Tammy M Havener
- UNC Catalyst for Rare Diseases, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Edward Anderson
- UNC Catalyst for Rare Diseases, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Daniel H Foil
- Collaborations Pharmaceuticals, Inc, 840 Main Campus Drive, Lab 3510, Raleigh, NC, USA
| | - Kimberley M Zorn
- Collaborations Pharmaceuticals, Inc, 840 Main Campus Drive, Lab 3510, Raleigh, NC, USA
| | | | - Olga Riabova
- Research Center of Biotechnology RAS, 119071 Moscow, Russia
| | - Anthony J Hickey
- Research Center of Biotechnology RAS, 119071 Moscow, Russia; RTI International, Research Triangle Park, NC, USA
| | - Vadim Makarov
- Research Center of Biotechnology RAS, 119071 Moscow, Russia
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc, 840 Main Campus Drive, Lab 3510, Raleigh, NC, USA.
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21
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Chaiwongkhot P, Zhong J, Huang A, Qin H, Shi SC, Makarov V. Faking photon number on a transition-edge sensor. EPJ Quantum Technol 2022; 9:23. [PMID: 36108324 PMCID: PMC9444832 DOI: 10.1140/epjqt/s40507-022-00141-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
We study potential security vulnerabilities of a single-photon detector based on superconducting transition-edge sensor. In one experiment, we show that an adversary could fake a photon number result at a certain wavelength by sending a larger number of photons at a longer wavelength, which is an expected and known behaviour. In another experiment, we unexpectedly find that the detector can be blinded by bright continuous-wave light and then, a controlled response simulating single-photon detection can be produced by applying a bright light pulse. We model an intercept-and-resend attack on a quantum key distribution system that exploits the latter vulnerability and, under certain assumptions, able to steal the key.
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Affiliation(s)
- Poompong Chaiwongkhot
- Institute for Quantum Computing, University of Waterloo, Waterloo, ON N2L 3G1 Canada
- Department of Physics and Astronomy, University of Waterloo, Waterloo, ON N2L 3G1 Canada
- Department of Physics, Faculty of Science, Mahidol University, Bangkok, 10400 Thailand
- Quantum Technology Foundation (Thailand), Bangkok, 10110 Thailand
| | - Jiaqiang Zhong
- Purple Mountain Observatory and Key Laboratory of Radio Astronomy, Chinese Academy of Sciences, 10 Yuanhua road, Nanjing, 210033 People’s Republic of China
| | - Anqi Huang
- Institute for Quantum Information & State Key Laboratory of High Performance Computing, College of Computer Science and Technology, National University of Defense Technology, Changsha, 410073 People’s Republic of China
| | - Hao Qin
- Centre for Quantum Technologies, National University of Singapore, 3 Science Drive 2, Singapore, 117543 Singapore
| | - Sheng-cai Shi
- Purple Mountain Observatory and Key Laboratory of Radio Astronomy, Chinese Academy of Sciences, 10 Yuanhua road, Nanjing, 210033 People’s Republic of China
| | - Vadim Makarov
- Russian Quantum Center, Skolkovo, Moscow, 121205 Russia
- Shanghai Branch, National Laboratory for Physical Sciences at Microscale and CAS Center for Excellence in Quantum Information, University of Science and Technology of China, Shanghai, 201315 People’s Republic of China
- NTI Center for Quantum Communications, National University of Science and Technology MISiS, Moscow, 119049 Russia
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22
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Riabova O, Egorova A, Lepioshkin A, Li Y, Voigt K, Kloss F, Makarov V. Thieno[2,3-d]pyrimidine-Core Compounds Show Activity Against Clinically Relevant Gram-Positive Bacteria. ChemMedChem 2022; 17:e202200207. [PMID: 35880634 DOI: 10.1002/cmdc.202200207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/20/2022] [Indexed: 11/09/2022]
Abstract
Thieno[2,3- d ]pyrimidines represent a novel antibacterial prodrug scaffold, previously identified through a screening campaign against Mycobacterium tuberculosis in which the formation of highly antimycobacterial metabolites catalyzed by the nitroreductase Mrx2 is suggested to be the relevant killing mechanism. As analogical activation pathways may also be employed in other prokaryotes, in this work we explored general antibacterial effects of this compound class. Through exploration of the chemical space by different synthetic strategies, 51 novel derivatives were generated, biologically evaluated and thus enabled initial conclusions about structure-activity-relationships. Remarkably, anti-Gram-positive activity can be well modulated, particularly towards Staphylococci (MRSA) and even slightly against some Gram-negative strains. The two most promising hit compounds showed good pharmacokinetic properties in vitro as well as acceptable toxicity in HeLa cells qualifying them as starting points for lead generation campaigns.
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Affiliation(s)
- Olga Riabova
- Research Center of Biotechnology RAS, Biomedicinal Chemistry, RUSSIAN FEDERATION
| | - Anna Egorova
- Research Center of Biotechnology RAS, Biomedicinal Chemistry, RUSSIAN FEDERATION
| | - Alexander Lepioshkin
- Research Center of Biotechnology RAS, Biomedicinal Chemistry, RUSSIAN FEDERATION
| | - Yan Li
- Leibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute: Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut, Transfer Group Anti-infectives, GERMANY
| | - Kerstin Voigt
- Leibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute: Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut, Jena Microbial Resource Collection, GERMANY
| | - Florian Kloss
- Leibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute: Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut, Transfer Group Anti-infectives, GERMANY
| | - Vadim Makarov
- Research Center of Biotechnology RAS, Biomedicinal Chemistry, Leninsky pr 33-2, 119071, Moscow, RUSSIAN FEDERATION
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23
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Puhl AC, Gomes GF, Damasceno S, Godoy AS, Noske GD, Nakamura AM, Gawriljuk VO, Fernandes RS, Monakhova N, Riabova O, Lane TR, Makarov V, Veras FP, Batah SS, Fabro AT, Oliva G, Cunha FQ, Alves-Filho JC, Cunha TM, Ekins S. Pyronaridine Protects against SARS-CoV-2 Infection in Mouse. ACS Infect Dis 2022; 8:1147-1160. [PMID: 35609344 PMCID: PMC9159503 DOI: 10.1021/acsinfecdis.2c00091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Indexed: 12/23/2022]
Abstract
There are currently relatively few small-molecule antiviral drugs that are either approved or emergency-approved for use against severe acute respiratory coronavirus 2 (SARS-CoV-2). One of these is remdesivir, which was originally repurposed from its use against Ebola. We evaluated three molecules we had previously identified computationally with antiviral activity against Ebola and Marburg and identified pyronaridine, which inhibited the SARS-CoV-2 replication in A549-ACE2 cells. The in vivo efficacy of pyronaridine has now been assessed in a K18-hACE transgenic mouse model of COVID-19. Pyronaridine treatment demonstrated a statistically significant reduction of viral load in the lungs of SARS-CoV-2-infected mice, reducing lung pathology, which was also associated with significant reduction in the levels of pro-inflammatory cytokines/chemokine and cell infiltration. Pyronaridine inhibited the viral PLpro activity in vitro (IC50 of 1.8 μM) without any effect on Mpro, indicating a possible molecular mechanism involved in its ability to inhibit SARS-CoV-2 replication. We have also generated several pyronaridine analogs to assist in understanding the structure activity relationship for PLpro inhibition. Our results indicate that pyronaridine is a potential therapeutic candidate for COVID-19.
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Affiliation(s)
- Ana C. Puhl
- Collaborations Pharmaceuticals,
Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606,
United States
| | - Giovanni F. Gomes
- Center for Research in Inflammatory Diseases (CRID),
Ribeirao Preto Medical School, University of São Paulo,
Avenida Bandeirantes, 3900, Ribeirao Preto 14049-900, São Paulo,
Brazil
| | - Samara Damasceno
- Center for Research in Inflammatory Diseases (CRID),
Ribeirao Preto Medical School, University of São Paulo,
Avenida Bandeirantes, 3900, Ribeirao Preto 14049-900, São Paulo,
Brazil
| | - Andre S. Godoy
- Institute of Physics of Sao Carlos,
University of São Paulo, Av. Joao Dagnone, 1100 -
Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Gabriela D. Noske
- Institute of Physics of Sao Carlos,
University of São Paulo, Av. Joao Dagnone, 1100 -
Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Aline M. Nakamura
- Institute of Physics of Sao Carlos,
University of São Paulo, Av. Joao Dagnone, 1100 -
Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Victor O. Gawriljuk
- Institute of Physics of Sao Carlos,
University of São Paulo, Av. Joao Dagnone, 1100 -
Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Rafaela S. Fernandes
- Institute of Physics of Sao Carlos,
University of São Paulo, Av. Joao Dagnone, 1100 -
Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Natalia Monakhova
- Research Center of Biotechnology
RAS, Leninsky prospect, 33, Building 2, 119071 Moscow,
Russia
| | - Olga Riabova
- Research Center of Biotechnology
RAS, Leninsky prospect, 33, Building 2, 119071 Moscow,
Russia
| | - Thomas R. Lane
- Collaborations Pharmaceuticals,
Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606,
United States
| | - Vadim Makarov
- Research Center of Biotechnology
RAS, Leninsky prospect, 33, Building 2, 119071 Moscow,
Russia
| | - Flavio P. Veras
- Center for Research in Inflammatory Diseases (CRID),
Ribeirao Preto Medical School, University of São Paulo,
Avenida Bandeirantes, 3900, Ribeirao Preto 14049-900, São Paulo,
Brazil
| | - Sabrina S. Batah
- Department of Pathology and Legal Medicine,
Ribeirão Preto Medical School, University of São
Paulo, Avenida Bandeirantes, 3900, Ribeirao Preto 14049-900, São
Paulo, Brazil
| | - Alexandre T. Fabro
- Department of Pathology and Legal Medicine,
Ribeirão Preto Medical School, University of São
Paulo, Avenida Bandeirantes, 3900, Ribeirao Preto 14049-900, São
Paulo, Brazil
| | - Glaucius Oliva
- Institute of Physics of Sao Carlos,
University of São Paulo, Av. Joao Dagnone, 1100 -
Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Fernando Q. Cunha
- Center for Research in Inflammatory Diseases (CRID),
Ribeirao Preto Medical School, University of São Paulo,
Avenida Bandeirantes, 3900, Ribeirao Preto 14049-900, São Paulo,
Brazil
| | - José C. Alves-Filho
- Center for Research in Inflammatory Diseases (CRID),
Ribeirao Preto Medical School, University of São Paulo,
Avenida Bandeirantes, 3900, Ribeirao Preto 14049-900, São Paulo,
Brazil
| | - Thiago M. Cunha
- Center for Research in Inflammatory Diseases (CRID),
Ribeirao Preto Medical School, University of São Paulo,
Avenida Bandeirantes, 3900, Ribeirao Preto 14049-900, São Paulo,
Brazil
| | - Sean Ekins
- Collaborations Pharmaceuticals,
Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606,
United States
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Popov A, Gridnev D, Gritskevich A, Trandofilov M, Islamova D, Makarov V, Vozny E. P-93 The role of combined treatment of metastatic colorectal cancer in patients with liver metastases. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.04.183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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25
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Popov A, Gridnev D, Gritskevich A, Makarov V, Islamova D, Vozny E, Kudryavtseva A. P-103 The importance of maintenance chemotherapy in the first and second line of treatment of metastatic colorectal cancer. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.04.193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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26
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Alimbarova L, Egorova A, Riabova O, Monakhova N, Makarov V. A proof-of-concept study for the efficacy of dispirotripiperazine PDSTP in a rabbit model of herpes simplex epithelial keratitis. Antiviral Res 2022; 202:105327. [PMID: 35487465 DOI: 10.1016/j.antiviral.2022.105327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 11/02/2022]
Abstract
Herpes simplex keratitis is an important infectious cause of blindness worldwide. The mainstay of antiviral therapy is treatment with long-established nucleoside analogues orally or topically. However, the emergence of resistant strains may become a major health concern in the future. Therefore, the development of backup antiherpetic medicines is urgently needed. Small molecule PDSTP is known to be active against herpes simplex type 1 strains in vitro, affecting early host-pathogen interactions. Here, we evaluated its preclinical efficacy in a rabbit model of herpes simplex epithelial keratitis. The mean course of keratitis and the corneal lesions in the 1.0% PDSTP gel group was statistically significantly less than in the negative control group and was comparable to that in the aciclovir group. These findings open up new opportunities for the development of antiherpetic drugs with an original mechanism of action.
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Affiliation(s)
- Lyudmila Alimbarova
- Gamaleya National Research Centre of Epidemiology and Microbiology of the Ministry of Health of Russia, 18 Gamaleya Street, 123098, Moscow, Russia
| | - Anna Egorova
- Research Centre of Biotechnology RAS, 33-2 Leninsky Prospect, 119071, Moscow, Russia
| | - Olga Riabova
- Research Centre of Biotechnology RAS, 33-2 Leninsky Prospect, 119071, Moscow, Russia
| | - Natalia Monakhova
- Research Centre of Biotechnology RAS, 33-2 Leninsky Prospect, 119071, Moscow, Russia
| | - Vadim Makarov
- Research Centre of Biotechnology RAS, 33-2 Leninsky Prospect, 119071, Moscow, Russia.
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27
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Lane TR, Urbina F, Rank L, Gerlach J, Riabova O, Lepioshkin A, Kazakova E, Vocat A, Tkachenko V, Cole S, Makarov V, Ekins S. Machine Learning Models for Mycobacterium tuberculosisIn Vitro Activity: Prediction and Target Visualization. Mol Pharm 2022; 19:674-689. [PMID: 34964633 PMCID: PMC9121329 DOI: 10.1021/acs.molpharmaceut.1c00791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB) is a major global health challenge, with approximately 1.4 million deaths per year. There is still a need to develop novel treatments for patients infected with Mycobacterium tuberculosis (Mtb). There have been many large-scale phenotypic screens that have led to the identification of thousands of new compounds. Yet, there is very limited investment in TB drug discovery which points to the need for new methods to increase the efficiency of drug discovery against Mtb. We have used machine learning approaches to learn from the public Mtb data, resulting in many data sets and models with robust enrichment and hit rates leading to the discovery of new active compounds. Recently, we have curated predominantly small-molecule Mtb data and developed new machine learning classification models with 18 886 molecules at different activity cutoffs. We now describe the further validation of these Bayesian models using a library of over 1000 molecules synthesized as part of EU-funded New Medicines for TB and More Medicines for TB programs. We highlight molecular features which are enriched in these active compounds. In addition, we provide new regression and classification models that can be used for scoring compound libraries or used to design new molecules. We have also visualized these molecules in the context of known molecular targets and identified clusters in chemical property space, which may aid in future target identification efforts. Finally, we are also making these data sets publicly available, representing a significant increase to the available Mtb inhibition data in the public domain.
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Affiliation(s)
- Thomas R. Lane
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510 Raleigh, NC 27606, USA
| | - Fabio Urbina
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510 Raleigh, NC 27606, USA
| | - Laura Rank
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510 Raleigh, NC 27606, USA
| | - Jacob Gerlach
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510 Raleigh, NC 27606, USA
| | - Olga Riabova
- Research Center of Biotechnology RAS, 119071 Moscow, Russia
| | | | - Elena Kazakova
- Research Center of Biotechnology RAS, 119071 Moscow, Russia
| | - Anthony Vocat
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Valery Tkachenko
- Science Data Experts, 14909 Forest Landing Cir, Rockville, MD 20850
| | | | - Vadim Makarov
- Research Center of Biotechnology RAS, 119071 Moscow, Russia
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510 Raleigh, NC 27606, USA
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28
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Schmalstig AA, Zorn KM, Murci S, Robinson A, Savina S, Komarova E, Makarov V, Braunstein M, Ekins S. Mycobacterium abscessus drug discovery using machine learning. Tuberculosis (Edinb) 2022; 132:102168. [PMID: 35077930 PMCID: PMC8855326 DOI: 10.1016/j.tube.2022.102168] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/30/2021] [Accepted: 01/14/2022] [Indexed: 01/22/2023]
Abstract
The prevalence of infections by nontuberculous mycobacteria is increasing, having surpassed tuberculosis in the United States and much of the developed world. Nontuberculous mycobacteria occur naturally in the environment and are a significant problem for patients with underlying lung diseases such as bronchiectasis, chronic obstructive pulmonary disease, and cystic fibrosis. Current treatment regimens are lengthy, complicated, toxic and they are often unsuccessful as seen by disease recurrence. Mycobacterium abscessus is one of the most commonly encountered organisms in nontuberculous mycobacteria disease and it is the most difficult to eradicate. There is currently no systematically proven regimen that is effective for treating M. abscessus infections. Our approach to drug discovery integrates machine learning, medicinal chemistry and in vitro testing and has been previously applied to Mycobacterium tuberculosis. We have now identified several novel 1-(phenylsulfonyl)-1H-benzimidazol-2-amines that have weak activity on M. abscessus in vitro but may represent a starting point for future further medicinal chemistry optimization. We also address limitations still to be overcome with the machine learning approach for M. abscessus.
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Affiliation(s)
- Alan A. Schmalstig
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, North Carolina, 27599, USA
| | - Kimberley M. Zorn
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive Lab 3510, Raleigh, North Carolina, 27606, USA
| | - Sebastian Murci
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, North Carolina, 27599, USA
| | - Andrew Robinson
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, North Carolina, 27599, USA
| | - Svetlana Savina
- Research Center of Biotechnology RAS, Moscow, 119071, Russia
| | - Elena Komarova
- Research Center of Biotechnology RAS, Moscow, 119071, Russia
| | - Vadim Makarov
- Research Center of Biotechnology RAS, Moscow, 119071, Russia
| | - Miriam Braunstein
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, North Carolina, 27599, USA
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive Lab 3510, Raleigh, North Carolina, 27606, USA.,Corresponding author: Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive Lab 3510, Raleigh, North Carolina, 27606, USA.
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29
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Glenn SM, Turapov O, Makarov V, Kell DB, Mukamolova GV. Dimethyl fumarate eliminates differentially culturable Mycobacterium tuberculosis in an intranasal murine model of tuberculosis. Front Cell Infect Microbiol 2022; 12:957287. [PMID: 36093181 PMCID: PMC9449328 DOI: 10.3389/fcimb.2022.957287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) claims nearly 1.5 million lives annually. Current TB treatment requires a combination of several drugs administered for at least 6 months. Mycobacterium tuberculosis (Mtb), the causative agent of TB, can persist in infected humans and animals for decades. Moreover, during infection, Mtb produces differentially culturable bacteria (DCB) that do not grow in standard media but can be resuscitated in liquid media supplemented with sterile Mtb culture filtrates or recombinant resuscitation-promoting factors (Rpfs). Here, we demonstrate that, in an intranasal murine model of TB, Mtb DCB are detectable in the lungs after 4 weeks of infection, and their loads remain largely unchanged during a further 8 weeks. Treatment of the infected mice with dimethyl fumarate (DMF), a known drug with immunomodulatory properties, for 8 weeks eliminates Mtb DCB from the lungs and spleens. Standard TB treatment consisting of rifampicin, isoniazid, and pyrazinamide for 8 weeks reduces Mtb loads by nearly four orders of magnitude but does not eradicate DCB. Nevertheless, no DCB can be detected in the lungs and spleens after 8 weeks of treatment with DMF, rifampicin, isoniazid, and pyrazinamide. Our data suggest that addition of approved anti-inflammatory drugs to standard treatment regimens may improve TB treatment and reduce treatment duration.
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Affiliation(s)
- Sarah M Glenn
- Division of Biomedical Services, University of Leicester, Leicester, United Kingdom
| | - Obolbek Turapov
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Vadim Makarov
- Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Douglas B Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom.,The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Galina V Mukamolova
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
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30
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Egorova A, Salina EG, Makarov V. Targeting Non-Replicating Mycobacterium tuberculosis and Latent Infection: Alternatives and Perspectives (Mini-Review). Int J Mol Sci 2021; 22:ijms222413317. [PMID: 34948114 PMCID: PMC8707483 DOI: 10.3390/ijms222413317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 01/02/2023] Open
Abstract
Latent tuberculosis infection (LTBI) represents a major challenge to curing TB disease. Current guidelines for LTBI management include only three older drugs and their combinations-isoniazid and rifamycins (rifampicin and rifapentine). These available control strategies have little impact on latent TB elimination, and new specific therapeutics are urgently needed. In the present mini-review, we highlight some of the alternatives that may potentially be included in LTBI treatment recommendations and a list of early-stage prospective small molecules that act on drug targets specific for Mycobacterium tuberculosis latency.
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Affiliation(s)
- Anna Egorova
- The Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences (Research Center of Biotechnology RAS), 119071 Moscow, Russia; (A.E.); (E.G.S.)
| | - Elena G. Salina
- The Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences (Research Center of Biotechnology RAS), 119071 Moscow, Russia; (A.E.); (E.G.S.)
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Vadim Makarov
- The Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences (Research Center of Biotechnology RAS), 119071 Moscow, Russia; (A.E.); (E.G.S.)
- Correspondence:
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31
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Gawriljuk VO, Foil DH, Puhl AC, Zorn KM, Lane TR, Riabova O, Makarov V, Godoy AS, Oliva G, Ekins S. Development of Machine Learning Models and the Discovery of a New Antiviral Compound against Yellow Fever Virus. J Chem Inf Model 2021; 61:3804-3813. [PMID: 34286575 DOI: 10.1021/acs.jcim.1c00460] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Yellow fever (YF) is an acute viral hemorrhagic disease transmitted by infected mosquitoes. Large epidemics of YF occur when the virus is introduced into heavily populated areas with high mosquito density and low vaccination coverage. The lack of a specific small molecule drug treatment against YF as well as for homologous infections, such as zika and dengue, highlights the importance of these flaviviruses as a public health concern. With the advancement in computer hardware and bioactivity data availability, new tools based on machine learning methods have been introduced into drug discovery, as a means to utilize the growing high throughput screening (HTS) data generated to reduce costs and increase the speed of drug development. The use of predictive machine learning models using previously published data from HTS campaigns or data available in public databases, can enable the selection of compounds with desirable bioactivity and absorption, distribution, metabolism, and excretion profiles. In this study, we have collated cell-based assay data for yellow fever virus from the literature and public databases. The data were used to build predictive models with several machine learning methods that could prioritize compounds for in vitro testing. Five molecules were prioritized and tested in vitro from which we have identified a new pyrazolesulfonamide derivative with EC50 3.2 μM and CC50 24 μM, which represents a new scaffold suitable for hit-to-lead optimization that can expand the available drug discovery candidates for YF.
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Affiliation(s)
- Victor O Gawriljuk
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100 - Santa Angelina, São Carlos, São Paulo 13563-120, Brazil
| | - Daniel H Foil
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Ana C Puhl
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Kimberley M Zorn
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Thomas R Lane
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Olga Riabova
- Research Center of Biotechnology RAS, Leninsky Prospekt 33-2, 119071 Moscow, Russia
| | - Vadim Makarov
- Research Center of Biotechnology RAS, Leninsky Prospekt 33-2, 119071 Moscow, Russia
| | - Andre S Godoy
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100 - Santa Angelina, São Carlos, São Paulo 13563-120, Brazil
| | - Glaucius Oliva
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100 - Santa Angelina, São Carlos, São Paulo 13563-120, Brazil
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
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32
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Gridnev D, Popov A, Makarov V, Islamova D, Vozny E, Kudryavtseva A. P-102 The importance of maintenance chemotherapy in the first and second lines of treatment of metastatic colorectal cancer. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.05.157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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33
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Donlin MJ, Lane TR, Riabova O, Lepioshkin A, Xu E, Lin J, Makarov V, Ekins S. Discovery of 5-Nitro-6-thiocyanatopyrimidines as Inhibitors of Cryptococcus neoformans and Cryptococcus gattii. ACS Med Chem Lett 2021; 12:774-781. [PMID: 34055225 DOI: 10.1021/acsmedchemlett.1c00038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/31/2021] [Indexed: 12/27/2022] Open
Abstract
Opportunistic infections from pathogenic fungi present a major challenge to healthcare because of a very limited arsenal of antifungal drugs, an increasing population of immunosuppressed patients, and increased prevalence of resistant clinical strains due to overuse of the few available antifungals. Cryptococcal meningitis is a life-threatening opportunistic fungal infection caused by one of two species in the Cryptococcus genus, Cryptococcus neoformans and Cryptococcus gattii. Eighty percent of cryptococcosis diseases are caused by C. neoformans that is endemic in the environment. The standard of care is limited to old antifungals, and under a high standard of care, mortality remains between 10 and 30%. We have identified a series of 5-nitro-6-thiocyanatopyrimidine antifungal drug candidates using in vitro and computational machine learning approaches. These compounds can inhibit C. neoformans growth at submicromolar levels, are effective against fluconazole-resistant C. neoformans and a clinical strain of C. gattii, and are not antagonistic with currently approved antifungals.
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Affiliation(s)
- Maureen J. Donlin
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, United States
- Institute for Drug and Biotherapeutic Development, Saint Louis University, St. Louis, Missouri 63103, United States
| | - Thomas R. Lane
- Collaborations Pharmaceuticals, Inc., Raleigh, North Carolina 27606, United States
| | - Olga Riabova
- Department of Biology, Saint Louis University, St. Louis, Missouri 63103, United States
| | - Alexander Lepioshkin
- Department of Biology, Saint Louis University, St. Louis, Missouri 63103, United States
| | - Evan Xu
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, United States
| | - Jeffrey Lin
- Department of Biology, Saint Louis University, St. Louis, Missouri 63103, United States
| | - Vadim Makarov
- Research Center of Biotechnology RAS, 119071 Moscow, Russia
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., Raleigh, North Carolina 27606, United States
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34
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Sajeed S, Chaiwongkhot P, Huang A, Qin H, Egorov V, Kozubov A, Gaidash A, Chistiakov V, Vasiliev A, Gleim A, Makarov V. An approach for security evaluation and certification of a complete quantum communication system. Sci Rep 2021; 11:5110. [PMID: 33658528 PMCID: PMC7930270 DOI: 10.1038/s41598-021-84139-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 02/12/2021] [Indexed: 11/18/2022] Open
Abstract
Although quantum communication systems are being deployed on a global scale, their realistic security certification is not yet available. Here we present a security evaluation and improvement protocol for complete quantum communication systems. The protocol subdivides a system by defining seven system implementation sub-layers based on a hierarchical order of information flow; then it categorises the known system implementation imperfections by hardness of protection and practical risk. Next, an initial analysis report lists all potential loopholes in its quantum-optical part. It is followed by interactions with the system manufacturer, testing and patching most loopholes, and re-assessing their status. Our protocol has been applied on multiple commercial quantum key distribution systems to improve their security. A detailed description of our methodology is presented with the example of a subcarrier-wave system. Our protocol is a step towards future security evaluation and security certification standards.
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Affiliation(s)
- Shihan Sajeed
- Institute for Quantum Computing, University of Waterloo, Waterloo, ON, N2L 3G1, Canada. .,Department of Physics and Astronomy, University of Waterloo, Waterloo, ON, N2L 3G1, Canada. .,Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON, N2L 3G1, Canada. .,Department of Electrical and Computer Engineering, University of Toronto, Toronto, M5S 3G4, Canada.
| | - Poompong Chaiwongkhot
- Institute for Quantum Computing, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.,Department of Physics and Astronomy, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.,Department of Physics, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Quantum Technology Foundation (Thailand), Bangkok, 10110, Thailand
| | - Anqi Huang
- Institute for Quantum Computing, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.,Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.,Institute for Quantum Information and State Key Laboratory of High Performance Computing, College of Computer Science and Technology, National University of Defense Technology, Changsha, 410073, People's Republic of China
| | - Hao Qin
- Institute for Quantum Computing, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.,CAS Quantum Network Co., Ltd., 99 Xiupu road, Shanghai, 201315, People's Republic of China
| | - Vladimir Egorov
- Faculty of Photonics and Optical Information, ITMO University, Kadetskaya line 3/2, 199034, St. Petersburg, Russia
| | - Anton Kozubov
- Faculty of Photonics and Optical Information, ITMO University, Kadetskaya line 3/2, 199034, St. Petersburg, Russia
| | - Andrei Gaidash
- Faculty of Photonics and Optical Information, ITMO University, Kadetskaya line 3/2, 199034, St. Petersburg, Russia
| | - Vladimir Chistiakov
- Faculty of Photonics and Optical Information, ITMO University, Kadetskaya line 3/2, 199034, St. Petersburg, Russia
| | - Artur Vasiliev
- Faculty of Photonics and Optical Information, ITMO University, Kadetskaya line 3/2, 199034, St. Petersburg, Russia
| | - Artur Gleim
- Faculty of Photonics and Optical Information, ITMO University, Kadetskaya line 3/2, 199034, St. Petersburg, Russia
| | - Vadim Makarov
- Department of Physics and Astronomy, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.,Shanghai Branch, National Laboratory for Physical Sciences at Microscale and CAS Center for Excellence in Quantum Information, University of Science and Technology of China, Shanghai, 201315, People's Republic of China
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35
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Egorova A, Jackson M, Gavrilyuk V, Makarov V. Pipeline of anti-Mycobacterium abscessus small molecules: Repurposable drugs and promising novel chemical entities. Med Res Rev 2021; 41:2350-2387. [PMID: 33645845 DOI: 10.1002/med.21798] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/01/2021] [Accepted: 02/17/2021] [Indexed: 12/13/2022]
Abstract
The Mycobacterium abscessus complex is a group of emerging pathogens that are difficult to treat. There are no effective drugs for successful M. abscessus pulmonary infection therapy, and existing drug regimens recommended by the British or the American Thoracic Societies are associated with poor clinical outcomes. Therefore, novel antibacterial drugs are urgently needed to contain this global threat. The current anti-M. abscessus small-molecule drug development process can be enhanced by two parallel strategies-discovery of compounds from new chemical classes and commercial drug repurposing. This review focuses on recent advances in the finding of novel small-molecule agents, and more particularly focuses on the activity, mode of action and structure-activity relationship of promising inhibitors from five different chemical classes-benzimidazoles, indole-2-carboxamides, benzothiazoles, 4-piperidinoles, and oxazolidionones. We further discuss some other interesting small molecules, such as thiacetazone derivatives and benzoboroxoles, that are in the early stages of drug development, and summarize current knowledge about the efficacy of repurposable drugs, such as rifabutin, tedizolid, bedaquiline, and others. We finally review targets of therapeutic interest in M. abscessus that may be worthy of future drug and adjunct therapeutic development.
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Affiliation(s)
- Anna Egorova
- Research Center of Biotechnology RAS, Moscow, Russia
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Colorado, Fort Collins, USA
| | | | - Vadim Makarov
- Research Center of Biotechnology RAS, Moscow, Russia
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36
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Monakhova N, Korduláková J, Vocat A, Egorova A, Lepioshkin A, Salina EG, Nosek J, Repková E, Zemanová J, Jurdáková H, Górová R, Roh J, Degiacomi G, Sammartino JC, Pasca MR, Cole ST, Mikušová K, Makarov V. Design and Synthesis of Pyrano[3,2- b]indolones Showing Antimycobacterial Activity. ACS Infect Dis 2021; 7:88-100. [PMID: 33352041 DOI: 10.1021/acsinfecdis.0c00622] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Latent Mycobacterium tuberculosis infection presents one of the largest challenges for tuberculosis control and novel antimycobacterial drug development. A series of pyrano[3,2-b]indolone-based compounds was designed and synthesized via an original eight-step scheme. The synthesized compounds were evaluated for their in vitro activity against M. tuberculosis strains H37Rv and streptomycin-starved 18b (SS18b), representing models for replicating and nonreplicating mycobacteria, respectively. Compound 10a exhibited good activity with MIC99 values of 0.3 and 0.4 μg/mL against H37Rv and SS18b, respectively, as well as low toxicity, acceptable intracellular activity, and satisfactory metabolic stability and was selected as the lead compound for further studies. An analysis of 10a-resistant M. bovis mutants disclosed a cross-resistance with pretomanid and altered relative amounts of different forms of cofactor F420 in these strains. Complementation experiments showed that F420-dependent glucose-6-phosphate dehydrogenase and the synthesis of mature F420 were important for 10a activity. Overall these studies revealed 10a to be a prodrug that is activated by an unknown F420-dependent enzyme in mycobacteria.
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Affiliation(s)
- Natalia Monakhova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russian Federation
| | | | - Anthony Vocat
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Anna Egorova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russian Federation
| | - Alexander Lepioshkin
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russian Federation
| | - Elena G. Salina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russian Federation
| | | | | | | | | | | | - Jaroslav Roh
- Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové 50005, Czech Republic
| | - Giulia Degiacomi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
| | - José Camilla Sammartino
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
| | - Maria Rosalia Pasca
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
| | - Stewart T. Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | | | - Vadim Makarov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russian Federation
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37
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Garcia-Escartin JC, Sajeed S, Makarov V. Correction: Attacking quantum key distribution by light injection via ventilation openingss. PLoS One 2020; 15:e0244010. [PMID: 33296422 PMCID: PMC7725349 DOI: 10.1371/journal.pone.0244010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Székely R, Rengifo-Gonzalez M, Singh V, Riabova O, Benjak A, Piton J, Cimino M, Kornobis E, Mizrahi V, Johnsson K, Manina G, Makarov V, Cole ST. 6,11-Dioxobenzo[ f]pyrido[1,2- a]indoles Kill Mycobacterium tuberculosis by Targeting Iron-Sulfur Protein Rv0338c (IspQ), A Putative Redox Sensor. ACS Infect Dis 2020; 6:3015-3025. [PMID: 32930569 DOI: 10.1021/acsinfecdis.0c00531] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Screening of a diversity-oriented compound library led to the identification of two 6,11-dioxobenzo[f]pyrido[1,2-a]indoles (DBPI) that displayed low micromolar bactericidal activity against the Erdman strain of Mycobacterium tuberculosis in vitro. The activity of these hit compounds was limited to tubercle bacilli, including the nonreplicating form, and to Mycobacterium marinum. On hit expansion and investigation of the structure activity relationship, selected modifications to the dioxo moiety of the DBPI scaffold were either neutral or led to reduction or abolition of antimycobacterial activity. To find the target, DBPI-resistant mutants of M. tuberculosis Erdman were raised and characterized first microbiologically and then by whole genome sequencing. Four different mutations, all affecting highly conserved residues, were uncovered in the essential gene rv0338c (ispQ) that encodes a membrane-bound protein, named IspQ, with 2Fe-2S and 4Fe-4S centers and putative iron-sulfur-binding reductase activity. With the help of a structural model, two of the mutations were localized close to the 2Fe-2S domain in IspQ and another in transmembrane segment 3. The mutant genes were recessive to the wild type in complementation experiments and further confirmation of the hit-target relationship was obtained using a conditional knockdown mutant of rv0338c in M. tuberculosis H37Rv. More mechanistic insight was obtained from transcriptome analysis, following exposure of M. tuberculosis to two different DBPI; this revealed strong upregulation of the redox-sensitive SigK regulon and genes induced by oxidative and thiol-stress. The findings of this investigation pharmacologically validate a novel target in tubercle bacilli and open a new vista for tuberculosis drug discovery.
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Affiliation(s)
- Rita Székely
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Monica Rengifo-Gonzalez
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Vinayak Singh
- MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, Anzio Road, Observatory 7925, Cape Town 7701, South Africa
| | - Olga Riabova
- FRC Fundamentals of Biotechnology, Russian Academy of Science, 119071 Moscow, Russian Federation
| | - Andrej Benjak
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Jérémie Piton
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Mena Cimino
- Microbial Individuality and Infection, Institut Pasteur, 75015 Paris, France
| | - Etienne Kornobis
- Biomics, C2RT, Institut Pasteur, 75015 Paris, France
- Hub Bioinformatique et Biostatistique, USR 3756 CNRS, Institut Pasteur, 75015 Paris, France
| | - Valerie Mizrahi
- MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, Anzio Road, Observatory 7925, Cape Town 7701, South Africa
| | - Kai Johnsson
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Giulia Manina
- Microbial Individuality and Infection, Institut Pasteur, 75015 Paris, France
| | - Vadim Makarov
- FRC Fundamentals of Biotechnology, Russian Academy of Science, 119071 Moscow, Russian Federation
| | - Stewart T. Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Microbial Individuality and Infection, Institut Pasteur, 75015 Paris, France
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Egorova A, Bogner E, Novoselova E, Zorn KM, Ekins S, Makarov V. Dispirotripiperazine-core compounds, their biological activity with a focus on broad antiviral property, and perspectives in drug design (mini-review). Eur J Med Chem 2020; 211:113014. [PMID: 33218683 PMCID: PMC7658596 DOI: 10.1016/j.ejmech.2020.113014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/26/2020] [Accepted: 11/08/2020] [Indexed: 12/31/2022]
Abstract
Viruses are obligate intracellular parasites and have evolved to enter the host cell. To gain access they come into contact with the host cell through an initial adhesion, and some viruses from different genus may use heparan sulfate proteoglycans for it. The successful inhibition of this early event of the infection by synthetic molecules has always been an attractive target for medicinal chemists. Numerous reports have yielded insights into the function of compounds based on the dispirotripiperazine scaffold. Analysis suggests that this is a structural requirement for inhibiting the interactions between viruses and cell-surface heparan sulfate proteoglycans, thus preventing virus entry and replication. This review summarizes our current knowledge about the early history of development, synthesis, structure-activity relationships and antiviral evaluation of dispirotripiperazine-based compounds and where they are going in the future.
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Affiliation(s)
- Anna Egorova
- Research Center of Biotechnology RAS, Leninsky Prospekt 33-2, 119071, Moscow, Russia
| | - Elke Bogner
- Institute of Virology, Charité Universitätsmedizin Berlin, Charité Campus Mitte, Chariteplatz 1, 10117, Berlin, Germany
| | - Elena Novoselova
- Research Center of Biotechnology RAS, Leninsky Prospekt 33-2, 119071, Moscow, Russia
| | - Kimberley M Zorn
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab, 3510, Raleigh, NC, USA
| | - Sean Ekins
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab, 3510, Raleigh, NC, USA
| | - Vadim Makarov
- Research Center of Biotechnology RAS, Leninsky Prospekt 33-2, 119071, Moscow, Russia.
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Chiarelli LR, Degiacomi G, Egorova A, Makarov V, Pasca MR. Nitric oxide-releasing compounds for the treatment of lung infections. Drug Discov Today 2020; 26:542-550. [PMID: 33181094 DOI: 10.1016/j.drudis.2020.10.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/01/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022]
Abstract
The spread of acquired drug resistance and of microorganisms naturally resistant to antibiotics is a major threat to global health, leading to an urgent need for novel antimicrobial compounds. Exogenous nitric oxide (NO) represents an attractive and promising antimicrobial approach, showing both bactericidal and biofilm dispersal activities. Numerous studies have been performed to develop NO donor scaffolds, including small molecules, macromolecular compounds, nanoparticles (NPs), and polymeric materials. This approach has resulted in successful outcomes, with some NO-releasing compounds entering clinical practice. In this review, we highlight the importance of this strategy, with a focus on lung infections.
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Affiliation(s)
- Laurent R Chiarelli
- Department of Biology and Biotechnology 'Lazzaro Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Giulia Degiacomi
- Department of Biology and Biotechnology 'Lazzaro Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Anna Egorova
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospekt 33-2, 119071, Moscow, Russia
| | - Vadim Makarov
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospekt 33-2, 119071, Moscow, Russia
| | - Maria Rosalia Pasca
- Department of Biology and Biotechnology 'Lazzaro Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy.
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Makarov V, Riabova O, Ekins S, Pluzhnikov N, Chepur S. The past, present and future of RNA respiratory viruses: influenza and coronaviruses. Pathog Dis 2020; 78:ftaa046. [PMID: 32860686 PMCID: PMC7499567 DOI: 10.1093/femspd/ftaa046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
Influenza virus and coronaviruses continue to cause pandemics across the globe. We now have a greater understanding of their functions. Unfortunately, the number of drugs in our armory to defend us against them is inadequate. This may require us to think about what mechanisms to address. Here, we review the biological properties of these viruses, their genetic evolution and antiviral therapies that can be used or have been attempted. We will describe several classes of drugs such as serine protease inhibitors, heparin, heparan sulfate receptor inhibitors, chelating agents, immunomodulators and many others. We also briefly describe some of the drug repurposing efforts that have taken place in an effort to rapidly identify molecules to treat patients with COVID-19. While we put a heavy emphasis on the past and present efforts, we also provide some thoughts about what we need to do to prepare for respiratory viral threats in the future.
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Affiliation(s)
- Vadim Makarov
- Federal Research Center Fundamentals of Biotechnology of the Russian Academy of Sciences, 33-2 Leninsky Prospect, Moscow 119071, Russia
| | - Olga Riabova
- Federal Research Center Fundamentals of Biotechnology of the Russian Academy of Sciences, 33-2 Leninsky Prospect, Moscow 119071, Russia
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA
| | - Nikolay Pluzhnikov
- State Research Institute of Military Medicine of the Ministry of Defence of the Russian Federation, St Petersburg 195043, Russia
| | - Sergei Chepur
- State Research Institute of Military Medicine of the Ministry of Defence of the Russian Federation, St Petersburg 195043, Russia
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Nikonenko B, Makarov V, Bocharova I, Korotetskaya M, Kondratieva E, Sterzhanova N, Apt A. Anti-TB efficacy of PBTZ169 in mice with different genetic susceptibility to infection. Tuberculosis (Edinb) 2020. [DOI: 10.1183/13993003.congress-2020.2805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Garcia-Escartin JC, Sajeed S, Makarov V. Attacking quantum key distribution by light injection via ventilation openings. PLoS One 2020; 15:e0236630. [PMID: 32745079 PMCID: PMC7398518 DOI: 10.1371/journal.pone.0236630] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 07/10/2020] [Indexed: 11/19/2022] Open
Abstract
Quantum cryptography promises security based on the laws of physics with proofs of security against attackers of unlimited computational power. However, deviations from the original assumptions allow quantum hackers to compromise the system. We present a side channel attack that takes advantage of ventilation holes in optical devices to inject additional photons that can leak information about the secret key. We experimentally demonstrate light injection on an ID Quantique Clavis2 quantum key distribution platform and show that this may help an attacker to learn information about the secret key. We then apply the same technique to a prototype quantum random number generator and show that its output is biased by injected light. This shows that light injection is a potential security risk that should be addressed during the design of quantum information processing devices.
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Affiliation(s)
| | - Shihan Sajeed
- Institute for Quantum Computing, University of Waterloo, Waterloo, ON, Canada
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON, Canada
- Department of Physics and Astronomy, University of Waterloo, Waterloo, ON, Canada
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada
| | - Vadim Makarov
- Department of Physics and Astronomy, University of Waterloo, Waterloo, ON, Canada
- Russian Quantum Center, Skolkovo, Moscow, Russia
- Shanghai Branch, National Laboratory for Physical Sciences at Microscale and CAS Center for Excellence in Quantum Information, University of Science and Technology of China, Shanghai, People’s Republic of China
- NTI Center for Quantum Communications, National University of Science and Technology MISiS, Moscow, Russia
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44
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Degiacomi G, Sammartino J, Urbani A, Riabova O, Muñoz LM, Chiarelli L, Manetti F, Ramon-Garcia S, Makarov V, Pasca M. P146 New weapons are necessary to fight Mycobacterium abscessus. J Cyst Fibros 2020. [DOI: 10.1016/s1569-1993(20)30481-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Abstract
Tuberculosis (TB) continues to claim the lives of around 1.7 million people per year. Most concerning are the reports of multidrug drug resistance. Paradoxically, this global health pandemic is demanding new therapies when resources and interest are waning. However, continued tuberculosis drug discovery is critical to address the global health need and burgeoning multidrug resistance. Many diverse classes of antitubercular compounds have been identified with activity in vitro and in vivo. Our analyses of over 100 active leads are representative of thousands of active compounds generated over the past decade, suggests that they come from few chemical classes or natural product sources. We are therefore repeatedly identifying compounds that are similar to those that preceded them. Our molecule-centered cheminformatics analyses point to the need to dramatically increase the diversity of chemical libraries tested and get outside of the historic Mtb property space if we are to generate novel improved antitubercular leads.
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Affiliation(s)
- Vadim Makarov
- FRC Fundamentals of Biotechnology, Russian Academy of Science, Moscow 119071, Russia
| | - Elena Salina
- FRC Fundamentals of Biotechnology, Russian Academy of Science, Moscow 119071, Russia
| | - Robert C Reynolds
- Department of Medicine, Division of Hematology and Oncology, University of Alabama at Birmingham, NP 2540 J, 1720 Second Avenue South, Birmingham, Alabama 35294-3300, United States
| | - Phyo Phyo Kyaw Zin
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States.,Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510 Raleigh, North Carolina 27606, United States
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Chiarelli LR, Scoffone VC, Trespidi G, Barbieri G, Riabova O, Monakhova N, Porta A, Manina G, Riccardi G, Makarov V, Buroni S. Chemical, Metabolic, and Cellular Characterization of a FtsZ Inhibitor Effective Against Burkholderia cenocepacia. Front Microbiol 2020; 11:562. [PMID: 32318042 PMCID: PMC7154053 DOI: 10.3389/fmicb.2020.00562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/16/2020] [Indexed: 12/02/2022] Open
Abstract
There is an urgent need for new antimicrobials to treat the opportunistic Gram-negative Burkholderia cenocepacia, which represents a problematic challenge for cystic fibrosis patients. Recently, a benzothiadiazole derivative, C109, was shown to be effective against the infections caused by B. cenocepacia and other Gram-negative and-positive bacteria. C109 has a promising cellular target, the cell division protein FtsZ, and a recently developed PEGylated formulation make it an attractive molecule to counteract Burkholderia infections. However, the ability of efflux pumps to extrude it out of the cell represents a limitation for its use. Here, more than 50 derivatives of C109 were synthesized and tested against Gram-negative species and the Gram-positive Staphylococcus aureus. In addition, their activity was evaluated on the purified FtsZ protein. The chemical, metabolic and cellular stability of C109 has been assayed using different biological systems, including quantitative single-cell imaging. However, no further improvement on C109 was achieved, and the role of efflux in resistance was further confirmed. Also, a novel nitroreductase that can inactivate the compound was characterized, but it does not appear to play a role in natural resistance. All these data allowed a deep characterization of the compound, which will contribute to a further improvement of its properties.
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Affiliation(s)
- Laurent R Chiarelli
- Laboratory of Molecular Microbiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Viola Camilla Scoffone
- Laboratory of Molecular Microbiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Gabriele Trespidi
- Laboratory of Molecular Microbiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Giulia Barbieri
- Laboratory of Molecular Microbiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Olga Riabova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - Natalia Monakhova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - Alessio Porta
- Organic Chemistry Section, Department of Chemistry, University of Pavia, Pavia, Italy
| | - Giulia Manina
- Microbial Individuality and Infection Group, Cell Biology and Infection Department, Institut Pasteur, Paris, France
| | - Giovanna Riccardi
- Laboratory of Molecular Microbiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Vadim Makarov
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - Silvia Buroni
- Laboratory of Molecular Microbiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
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Volobueva A, Egorova A, Galochkina A, Ekins S, Zarubaev V, Makarov V. The Evolution of Pleconaril: Modified O-Alkyl Linker Analogs Have Biological Activity towards Coxsackievirus B3 Nancy. Molecules 2020; 25:molecules25061345. [PMID: 32188089 PMCID: PMC7144106 DOI: 10.3390/molecules25061345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 11/16/2022] Open
Abstract
Coxsackieviruses type B are one of the most common causes of mild upper respiratory and gastrointestinal illnesses. At the time of writing, there are no approved drugs for effective antiviral treatment for Coxsackieviruses type B. We used the core-structure of pleconaril, a well-known antienteroviral drug candidate, for the synthesis of novel compounds with O-propyl linker modifications. Some original compounds with 4 different linker patterns, such as sulfur atom, ester, amide, and piperazine, were synthesized according to five synthetic schemes. The cytotoxicity and bioactivity of 14 target compounds towards Coxsackievirus B3 Nancy were examined. Based on the results, the values of 50% cytotoxic dose (CC50), 50% virus-inhibiting dose (IC50), and selectivity index (SI) were calculated for each compound. Several of the novel synthesized derivatives exhibited a strong anti-CVB3 activity (SI > 20 to > 200). These results open up new possibilities for synthesis of further new selective anticoxsackievirus compounds.
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Affiliation(s)
- Alexandrina Volobueva
- Saint-Petersburg Pasteur Institute, Mira str., 14, 197101 Saint Petersburg, Russia; (A.V.); (A.G.); (V.Z.)
| | - Anna Egorova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prospect, 33, build. 2, 119071 Moscow, Russia;
| | - Anastasia Galochkina
- Saint-Petersburg Pasteur Institute, Mira str., 14, 197101 Saint Petersburg, Russia; (A.V.); (A.G.); (V.Z.)
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA;
| | - Vladimir Zarubaev
- Saint-Petersburg Pasteur Institute, Mira str., 14, 197101 Saint Petersburg, Russia; (A.V.); (A.G.); (V.Z.)
| | - Vadim Makarov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prospect, 33, build. 2, 119071 Moscow, Russia;
- Correspondence:
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Mori G, Orena BS, Chiarelli LR, Degiacomi G, Riabova O, Sammartino JC, Makarov V, Riccardi G, Pasca MR. Rv0579 Is Involved in the Resistance to the TP053 Antitubercular Prodrug. Front Microbiol 2020; 11:292. [PMID: 32158439 PMCID: PMC7052010 DOI: 10.3389/fmicb.2020.00292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/10/2020] [Indexed: 11/25/2022] Open
Abstract
Tuberculosis remains one of the leading causes of death from a single pathogen globally. It is estimated that 1/4 of the world’s population harbors latent tuberculosis, but only a 5–10% of patients will develop active disease. During latent infection, Mycobacterium tuberculosis can persist unaffected by drugs for years in a non-replicating state with low metabolic activity. The rate of the successful tuberculosis treatment is curbed by the presence of these non-replicating bacilli that can resuscitate after decades and also by the spread of M. tuberculosis drug-resistant strains. International agencies, including the World Health Organization, urge the international community to combat this global health emergency. The thienopyrimidine TP053 is a promising new antitubercular lead compound highly active against both replicating and non-replicating M. tuberculosis cells, with an in vitro MIC of 0.125 μg/ml. TP053 is a prodrug activated by the reduced form of the mycothiol-dependent reductase Mrx2, encoded by Rv2466c gene. After its activation, TP053 releases nitric oxide and a highly reactive metabolite, explaining its activity also against M. tuberculosis non-replicating cells. In this work, a new mechanism of TP053 resistance was discovered. M. tuberculosis spontaneous mutants resistant to TP053 were isolated harboring the mutation L240V in Rv0579, a protein with unknown function, but without mutation in Rv2466c gene. Recombineering method demonstrated that this mutation is linked to TP053 resistance. To better characterize Rv0579, the protein was recombinantly produced in Escherichia coli and a direct interaction between the Mrx2 activated TP053 and Rv0579 was shown by an innovative target-fishing experiment based on click chemistry. Thanks to achieved results, a possible contribution of Rv0579 in M. tuberculosis RNA metabolism was hypothesized, linked to toxin anti-toxin system. Overall, these data confirm the role of Rv0579 in TP053 resistance and consequently in the metabolism of this prodrug.
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Affiliation(s)
- Giorgia Mori
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
| | - Beatrice Silvia Orena
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
| | - Giulia Degiacomi
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
| | - Olga Riabova
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - José Camilla Sammartino
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
| | - Vadim Makarov
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - Giovanna Riccardi
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
| | - Maria Rosalia Pasca
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
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49
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Chiarelli LR, Salina EG, Mori G, Azhikina T, Riabova O, Lepioshkin A, Grigorov A, Forbak M, Madacki J, Orena BS, Manfredi M, Gosetti F, Buzzi A, Degiacomi G, Sammartino JC, Marengo E, Korduláková J, Riccardi G, Mikušová K, Makarov V, Pasca MR. New Insights into the Mechanism of Action of the Thienopyrimidine Antitubercular Prodrug TP053. ACS Infect Dis 2020; 6:313-323. [PMID: 31729215 DOI: 10.1021/acsinfecdis.9b00388] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The thienopyrimidine TP053 is an antitubercular prodrug active against both replicating and nonreplicating Mycobacterium tuberculosis (M. tuberculosis) cells, which requires activation by the mycothiol-dependent nitroreductase Mrx2. The investigation of the mechanism of action of TP053 revealed that Mrx2 releases nitric oxide from this drug both in the enzyme assays with purified Mrx2 and in mycobacterial cultures, which can explain its activity against nonreplicating bacilli, similar to pretomanid activated by the nitroreductase Ddn. In addition, we identified a highly reactive metabolite, 2-(4-mercapto-6-(methylamino)-2-phenylpyrimidin-5-yl)ethan-1-ol, which can contribute to the antimycobacterial effects on replicating cells as well as on nonreplicating cells. In summary, we explain the mechanism of action of TP053 on both replicating and nonreplicating M. tuberculosis and report a novel activity for Mrx2, which in addition to Ddn, represents another example of nitroreductase releasing nitric oxide from its substrate. These findings are particularly relevant in the context of drugs targeting nonreplicating M. tuberculosis, which is shown to be killed by increased levels of nitric oxide.
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Affiliation(s)
- Laurent R. Chiarelli
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, Pavia 27100, Italy
| | - Elena G. Salina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prospekt 33-2, Moscow 119071, Russia
| | - Giorgia Mori
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, Pavia 27100, Italy
| | - Tatyana Azhikina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Street, Moscow 117997, Russia
| | - Olga Riabova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prospekt 33-2, Moscow 119071, Russia
| | - Alexander Lepioshkin
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prospekt 33-2, Moscow 119071, Russia
| | - Artem Grigorov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Street, Moscow 117997, Russia
| | - Martin Forbak
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, CH1, Bratislava SK-842 15, Slovakia
| | - Jan Madacki
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, CH1, Bratislava SK-842 15, Slovakia
| | - Beatrice Silvia Orena
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, Pavia 27100, Italy
| | - Marcello Manfredi
- Department of Translational Medicine, Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, Corso Trieste 15, Novara 28100, Italy
- ISALIT, Spin-off of Department of Sciences and Technological Innovation, Via A. Canobio 4/6, Novara 28100, Italy
| | - Fabio Gosetti
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Teresa Michel 11, Alessandria 15121, Italy
| | - Arianna Buzzi
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Teresa Michel 11, Alessandria 15121, Italy
| | - Giulia Degiacomi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, Pavia 27100, Italy
| | - José Camilla Sammartino
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, Pavia 27100, Italy
| | - Emilio Marengo
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Teresa Michel 11, Alessandria 15121, Italy
| | - Jana Korduláková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, CH1, Bratislava SK-842 15, Slovakia
| | - Giovanna Riccardi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, Pavia 27100, Italy
| | - Katarína Mikušová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, CH1, Bratislava SK-842 15, Slovakia
| | - Vadim Makarov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prospekt 33-2, Moscow 119071, Russia
| | - Maria Rosalia Pasca
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, via Ferrata 9, Pavia 27100, Italy
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Buroni S, Makarov V, Scoffone VC, Trespidi G, Riccardi G, Chiarelli LR. The cell division protein FtsZ as a cellular target to hit cystic fibrosis pathogens. Eur J Med Chem 2020; 190:112132. [PMID: 32066012 DOI: 10.1016/j.ejmech.2020.112132] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/31/2020] [Accepted: 02/06/2020] [Indexed: 11/25/2022]
Abstract
Cystic fibrosis is a rare genetic disease characterized by the production of dehydrated mucus in the lung able to trap bacteria and rendering their proliferation particularly dangerous, thus leading to chronic infections. Among these bacteria, Staphylococcus aureus and Pseudomonas aeruginosa play a major role while, within emerging pathogens, Stenotrophomonas maltophilia, Achromobacter xylosoxidans, Burkholderia cepacia complex species, as well as non-tuberculous mycobacteria are listed. Since a common feature of these bacteria is the high level of drug resistance, cell division, and in particular FtsZ, has been explored as a novel therapeutic target for the design of new molecules with antibacterial properties. This review summarizes and provides insight into recent advances in the discovery of compounds targeting FtsZ: the majority of them exhibit anti-staphylococcal activity, while a few were directed against the cystic fibrosis Gram negative pathogens.
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Affiliation(s)
- Silvia Buroni
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Vadim Makarov
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - Viola Camilla Scoffone
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Gabriele Trespidi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Giovanna Riccardi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy.
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