Makarov LaboratoryMakarovLab

Neuroactive molecules

An alkaloid-like small molecule for cognitive impairment therapy

The project searches for a small-molecule candidate for cognitive impairment associated with depressive disorders and other CNS diseases.

The central chemical core is vindeburnol, a synthetic derivative inspired by eburnamine-vincamine alkaloids. Medicinal chemistry work is focused on fine-tuning this core and identifying a molecule that improves memory and reduces depression-like behavior. Lead selection includes in vitro ADME-T studies, blood-brain barrier permeability assessment, and biochemical analysis of monoamine levels in brain regions.To elucidate the lead compound's mechanism of action, we plan to conduct receptor binding assays. The project is being carried out in collaboration with the V. Serbsky National Medical Research Center for Psychiatry and Narcology and with financial support from "R-Pharm".

Vindeburnol project and behavioral testing scheme
Vindeburnol and behavioral models

Antiviral agents

Non-nucleoside reverse transcriptase inhibitors of HIV-1

A search for original inhibitors with improved efficacy and safety for antiretroviral therapy.

The project focuses on compounds that block reverse transcriptase and stop viral replication. More than one hundred derivatives were tested to understand structure-activity relationships. The work identified compound 12126065 with high in vitro activity against wild-type and clinical mutant HIV strains. The compound has been shown to be non-toxic and to possess good bioavailability. Moreover, it lacks the neurotoxicity associated with the standard drug efavirenz. Our next steps focus on evaluating the compound's efficacy in animal studies. This research project is being conducted in collaboration with Collaboration Pharmaceuticals (USA), the University of North Carolina (USA), and the University of Cagliari (Italy).

Key publications
  1. N-Phenyl-1-(phenylsulfonyl)-1H-1,2,4-triazol-3-amine as a new class of HIV-1 non-nucleoside reverse transcriptase inhibitor. Journal of Medicinal Chemistry, 2023
  2. New targets for HIV drug discovery. Drug Discovery Today, 2019
  3. Multiple machine learning comparisons of HIV cell-based and reverse transcriptase datasets. Molecular Pharmaceutics, 2019
Video material about HIV research
Molecular schemes and cell tests for HIV-1 inhibitors
Molecular design and cellular safety

Oncology

Small-molecule protein kinase inhibitors

Development of next-generation candidates for combination therapy of cancer diseases.

Cancer is one of the leading causes of death worldwide. It is known that cancer cells eventually develop resistance to existing drugs. To address this issue, it is necessary to develop next-generation inhibitors and improve combination therapies. The project aims to discover and develop a safe and effective drug candidate based on a thiophene scaffold for the treatment of a specific type of cancer. We employ NCI60 screening to conduct early-stage studies on the structure-activity relationship of the chemical class under investigation.Certain molecules from our laboratory's library inhibit the growth of melanoma and central nervous system cancer cells by up to 85% in vitro. We are currently profiling protein kinase inhibitors and conducting in vitro ADME-T studies to select the most promising molecules for in vivo toxicity and efficacy testing. The project is being conducted in partnership with Collaboration Pharmaceuticals (USA).

Key publications
  1. Multiple approaches to repurposing drugs for neuroblastoma. Bioorganic and Medicinal Chemistry, 2022
Protein kinase inhibitor project description
Thiophene scaffold and early screening

Tuberculosis

Inhibitors of resuscitation factors in dormant M. tuberculosis

A search for small molecules targeting proteins that trigger dormant mycobacteria reactivation.

Спящее состояние — одно из основных опасений предотвращения Mycobacterium Tuberculosis , позволяющее избежать их ликвидации, то есть полного удаления из организма человека. В этом состоянии так называемые спящие бактерии Mtb обладают сниженной чувствительностью к стандартным противотуберкулезным препаратам, но способны "просыпаться" и переходить в активное состояние, тем самым провоцируя рецидив туберкулезной инфекции. Известно, что в таком процессе реактивации реализованы «факторы индикатория» (факторы, способствующие оживлению, или Rpf) — секреторные белки, способствующие реанимации спивших микобактерий. Наш проект по поиску низкомолекулярных химических зондов, электрически воздействующих на этот белок, для того, чтобы найти более направленные соединения, способные соединители по Rpf-опосредованному "оживляющему воздействию" микобактерий. Это исследование проводится в Университете Лестера (Университет Лестера, Великобритания).

Key publications
  1. Dimethyl fumarate eliminates differentially culturable Mycobacterium tuberculosis in an intranasal murine model of tuberculosis. Frontiers in Cellular and Infection Microbiology, 2022
  2. Benzoylphenyl thiocyanates are new, effective inhibitors of the mycobacterial resuscitation promoting factor B protein. Annals of Clinical Microbiology and Antimicrobials, 2017
  3. The in vivo environment accelerates generation of resuscitation-promoting factor-dependent mycobacteria. American Journal of Respiratory and Critical Care Medicine, 2014
  4. Finding of the low molecular weight inhibitors of resuscitation promoting factor enzymatic and resuscitation activity. PLoS One, 2009
Mycobacteria illustration and resuscitation factor description
Image generated with Kandinsky 2.1

Antiviral agents

Dispirotripiperazine as an unusual scaffold for new antiviral agents

A tricyclic molecular class studied for blocking viral entry into host cells.

Dispirotripiperazines are tricyclic molecules featuring two shared atoms, or "spiro-atoms." A distinctive structural feature of these compounds is the presence of two positively charged nitrogen atoms; the precise significance of these atoms is not yet fully understood and forms part of the focus of our research. It is hypothesized that these atoms facilitate electrostatic interactions with negatively charged heparan sulfate residues on the host cell surface, thereby preventing viruses from entering the cell to replicate. The PDSTP molecule—the most potent representative of this chemical class to date—inhibits, in vitro, a range of known viruses that utilize heparan sulfate to interact with host cells. It has recently demonstrated efficacy in rabbit models of herpetic keratitis. This research is being conducted in the UK in collaboration with Charité – Universitätsmedizin Berlin and the University of Cagliari.

Key publications
  1. Antiviral evaluation of dispirotripiperazines against hepatitis B virus. Journal of Medicinal Chemistry, 2023
  2. A proof-of-concept study for the efficacy of dispirotripiperazine PDSTP in a rabbit model of herpes simplex epithelial keratitis. Antiviral Research, 2022
  3. Broad-spectrum antiviral diazadispiroalkane core molecules block attachment and cell-to-cell spread of herpesviruses. Antiviral Research, 2022
  4. Diazadispiroalkane derivatives are new viral entry inhibitors. Antimicrobial Agents Chemotherapy, 2021
  5. DSTP-27 prevents entry of human cytomegalovirus. Antimicrobial Agents Chemotherapy, 2014
PDSTP structure and efficacy charts
PDSTP scaffold and preclinical models

Antibacterial agents

Probe molecule C109 blocking the FtsZ protein in bacteria

Research on an inhibitor of a key cell division protein in pathogenic bacteria.

The filamenting temperature-sensitive mutant Z protein (FtsZ) is a key cell division protein in several pathogens—including Acinetobacter baumannii, Pseudomonas aeruginosa, Staphylococcus aureus (all on the WHO priority pathogen list), and Burkholderia cenocepacia. Screening of our in-house library identified a benzothiadiazole compound, C109, which effectively inhibits the growth of B. cenocepacia, P. aeruginosa, S. aureus, and A. baumannii. Furthermore, this molecule effectively blocks the GTPase activity of the FtsZ protein, making it a promising starting point for the discovery of novel antibacterial agents. This project is being conducted in collaboration with the University of Pavia (Italy).

Key publications
  1. Bactericidal and anti-biofilm activity of the FtsZ inhibitor C109 against Acinetobacter baumannii. Antibiotics, 2022
  2. Antistaphylococcal activity of the FtsZ inhibitor C109. Pathogens, 2021
  3. The cell division protein FtsZ as a cellular target to hit cystic fibrosis pathogens. European Journal of Medicinal Chemistry, 2020
  4. Chemical, metabolic, and cellular characterization of a FtsZ inhibitor effective against Burkholderia cenocepacia. Frontiers in Microbiology, 2020
  5. Competitive fitness of essential gene knockdowns reveals a broad-spectrum antibacterial inhibitor of the cell division protein FtsZ. Antimicrobial Agents Chemotherapy, 2018
  6. Efflux-mediated resistance to a benzothiadiazol derivative effective against Burkholderia cenocepacia. Frontiers in Microbiology, 2015
C109 scheme and biofilm microscopy images
C109 and biofilm microscopy

Tuberculosis

Probe molecule TP053 inhibiting active and dormant M. tuberculosis forms

A thienopyrimidine class studied against replicating and non-replicating mycobacteria.

Inspired by interesting pharmacological compounds containing the thieno[2,3-d]pyrimidine scaffold, we decided to investigate this chemical class against M. tuberculosis. Structure-activity relationship studies led to the identification of TP053 compounds, which exhibit low minimum inhibitory concentration values ​​against both replicating (H37Rv) and non-replicating (ss18b) forms of M. tuberculosis. TP053 acts as a prodrug against Mtb H37Rv through activation by the mycothiol-dependent nitroreductase Mrx2. The transformation of TP053 involves the condensation of the fused thiophene ring and the release of nitric oxide, an agent long known to be active against non-replicating forms of Mtb. At the same time, the resulting highly reactive metabolite exhibits activity against replicating mycobacteria. This project is being carried out in collaboration with the University of Pavia (Italy).

Key publications
  1. New insights into the mechanism of action of the thienopyrimidine antitubercular prodrug TP053. ACS Infectious Diseases, 2020
  2. Rv0579 is involved in the resistance to the TP053 antitubercular prodrug. Frontiers in Microbiology, 2020
  3. The antibacterial prodrug activator Rv2466c is a mycothiol-dependent reductase in the oxidative stress response of Mycobacterium tuberculosis. Journal of Biological Chemistry, 2017
  4. The redox state regulates the conformation of Rv2466c to activate the antitubercular prodrug TP053. Journal of Biological Chemistry, 2015
  5. Rv2466c mediates the activation of TP053 to kill replicating and non-replicating Mycobacterium tuberculosis. ACS Chemical Biology, 2014
TP053 structure and molecular model
TP053 and activation mechanism

Rhinoviruses

Picornaviridae capsid-binding small-molecule agents

Development of molecules targeting the capsid pocket of rhino- and enteroviruses.

The common cold—an acute inflammatory disease of the upper respiratory tract—is caused exclusively by enteroviruses and rhinoviruses. These viruses, which belong to the Picornaviridae family, feature a so-called "pocket" on the surface of their capsid; this pocket is responsible for the virus attaching to the host cell and initiating infection. Notably, this pocket serves as a binding site for small molecules. The mechanism of action for such molecules involves displacing the endogenous "pocket factor" by binding to the pocket much more tightly, thereby blocking an early stage of the viral life cycle: attachment to the cell. Our goal is to design molecules using a dynamic complex-formation mechanism that addresses the structure-activity relationship of two distinct small-molecule scaffolds at a detailed level. We are conducting in-depth studies of OBR-5-340 (based on a pyrazolo[3,4-d]pyrimidine core) and compound 10g (based on a pleconaril core; see Reference 4), both of which have been identified as lead molecules. It was also recently discovered, unexpectedly, that OBR-5-340 (designated SCO-201) can act as a modulator of ATP-binding cassette transporters, thereby resensitizing drug-resistant cancer to anticancer drugs.

Key publications
  1. Novel pleconaril derivatives: Influence of substituents in the isoxazole and phenyl rings on the antiviral activity against enteroviruses. European Journal of Medicinal Chemistry, 2020
  2. Cryo-EM structure of pleconaril-resistant rhinovirus-B5 complexed to the antiviral OBR-5-340 reveals unexpected binding site. PNAS, 2019
  3. Pyrazolopyrimidines: potent inhibitors targeting the capsid of rhino- and enteroviruses. ChemMedChem, 2015
  4. New pleconaril and [(biphenyloxy)propyl]isoxazole derivatives with substitutions in the central ring exhibit antiviral activity against pleconaril-resistant coxsackievirus B3. Antiviral Research, 2009
Molecules and Picornaviridae capsid-binding site
Capsid pocket and molecular binding

Tuberculosis

Benzothiazinones as a promising class of anti-tuberculosis agents

A strong anti-TB class discovered with partners and the development of lead compound PBTZ169.

We have long been interested in the development of effective anti-tuberculosis drugs. In 2007–2008, working with several team leaders and with financial support from the commission, we discovered the class of benzothiazinones as potent anti-tuberculosis agents. Molecules of this class served as chemical probes for the discovery of a new target in the tuberculosis bacillus—the enzyme decaprenylphosphoryl-β-D-ribose-2'-epimerase (DprE1), which plays a key role in mycobacterial cell wall synthesis and, consequently, in bacterial growth. During the optimization of the hit compound BTZ043, the lead compound PBTZ169 was developed. This molecule exhibits greater in vitro activity against multidrug-resistant and extensively drug-resistant M. tuberculosis strains, as well as other isolates. PBTZ169—which was assigned the INN "macozinone" in 2018—has demonstrated safety and efficacy not only in animal models (preclinical studies) but also in human trials (NCT03423030, NCT03036163, NCT03776500, NCT04150224, NCT03334734).

Key publications
  1. Development of macozinone for TB treatment: an update. Applied Science, 2020
  2. Optimized background regimen for treatment of active tuberculosis with the next-generation benzothiazinone macozinone (PBTZ169). Antimicrobial Agents Chemotherapy, 2018
  3. Towards a new combination therapy for tuberculosis with next generation benzothiazinones. EMBO Molecular Medicine, 2014
  4. Benzothiazinones are suicide inhibitors of mycobacterial decaprenylphosphoryl-β-D-ribofuranose 2'-oxidase DprE1. Journal of American Chemical Society, 2012
  5. Benzothiazinones: products that covalently modify the decaprenylphosphoryl-β-D-ribose 2'-epimerase DprE1 of Mycobacterium tuberculosis. Journal of American Chemical Society, 2010
  6. Benzothiazinones kill Mycobacterium tuberculosis by blocking arabinan synthesis. Science, 2009
Video about anti-tuberculosis research
PBTZ169 and DprE1 molecular model
PBTZ169, DprE1, and macozinone development