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Article ; Online: Monitoring Protein Complexation with Polyphosphazene Polyelectrolyte Using Automated Dynamic Light Scattering Titration and Asymmetric Flow Field Flow Fractionation and Protein Recognition Immunoassay.

Lueckheide, Michael / Marin, Alexander / Tagad, Harichandra D / Posey, Nicholas D / Prabhu, Vivek M / Andrianov, Alexander K

ACS polymers Au

2023 Volume 3, Issue 5, Page(s) 354–364

Abstract: Polyphosphazenes represent a class of intrinsically flexible polyelectrolytes with potent immunoadjuvant activity, which is enabled through non-covalent self-assembly with antigenic proteins by charge complexation. The formation of supramolecular ... ...

Abstract	Polyphosphazenes represent a class of intrinsically flexible polyelectrolytes with potent immunoadjuvant activity, which is enabled through non-covalent self-assembly with antigenic proteins by charge complexation. The formation of supramolecular complexes between polyphosphazene adjuvant, poly[di(carboxylatophenoxy)phosphazene] (PCPP), and a model vaccine antigen, hen egg lysozyme, was studied under physiological conditions using automated dynamic light scattering titration, asymmetric flow field flow fractionation (AF4), enzyme-linked immunosorbent assay (ELISA), and fluorescent quenching methods. Three regimes of self-assembly were observed covering complexation of PCPP with lysozyme in the nano-scale range, multi-chain complexes, and larger aggregates with complexes characterized by a maximum loading of over six hundred protein molecules per PCPP chain and dissociation constant in the micromolar range (
Language	English
Publishing date	2023-04-21
Publishing country	United States
Document type	Journal Article
ISSN	2694-2453
ISSN (online)	2694-2453
DOI	10.1021/acspolymersau.3c00006
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Article ; Online: AI-Driven De Novo Design and Molecular Modeling for Discovery of Small-Molecule Compounds as Potential Drug Candidates Targeting SARS-CoV-2 Main Protease.

Andrianov, Alexander M / Shuldau, Mikita A / Furs, Konstantin V / Yushkevich, Artsemi M / Tuzikov, Alexander V

International journal of molecular sciences

2023 Volume 24, Issue 9

Abstract: Over the past three years, significant progress has been made in the development of novel promising drug candidates against COVID-19. However, SARS-CoV-2 mutations resulting in the emergence of new viral strains that can be resistant to the drugs used ... ...

Abstract	Over the past three years, significant progress has been made in the development of novel promising drug candidates against COVID-19. However, SARS-CoV-2 mutations resulting in the emergence of new viral strains that can be resistant to the drugs used currently in the clinic necessitate the development of novel potent and broad therapeutic agents targeting different vulnerable spots of the viral proteins. In this study, two deep learning generative models were developed and used in combination with molecular modeling tools for de novo design of small molecule compounds that can inhibit the catalytic activity of SARS-CoV-2 main protease (Mpro), an enzyme critically important for mediating viral replication and transcription. As a result, the seven best scoring compounds that exhibited low values of binding free energy comparable with those calculated for two potent inhibitors of Mpro, via the same computational protocol, were selected as the most probable inhibitors of the enzyme catalytic site. In light of the data obtained, the identified compounds are assumed to present promising scaffolds for the development of new potent and broad-spectrum drugs inhibiting SARS-CoV-2 Mpro, an attractive therapeutic target for anti-COVID-19 agents.
MeSH term(s)	Artificial Intelligence ; Models, Molecular ; Small Molecule Libraries/pharmacology ; Small Molecule Libraries/therapeutic use ; Coronavirus 3C Proteases/antagonists & inhibitors ; Drug Discovery/methods ; Neural Networks, Computer ; COVID-19 Drug Treatment
Chemical Substances	Small Molecule Libraries ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
Language	English
Publishing date	2023-04-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24098083
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Article ; Online: Virtual screening and identification of promising therapeutic compounds against drug-resistant

Andrianov, Alexander M / Furs, Konstantin V / Gonchar, Anna V / Skrahina, Alena M / Wang, Yixin / Lyu, Liang-Dong / Tuzikov, Alexander V

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–13

Abstract: The emergence of ... ...

Abstract	The emergence of new
Language	English
Publishing date	2023-12-13
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2293276
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Article ; Online: Polyphosphazene: A New Adjuvant Platform for Cocaine Vaccine Development.

Lin, Mingliang / Marin, Alexander / Ellis, Beverly / Eubanks, Lisa M / Andrianov, Alexander K / Janda, Kim D

Molecular pharmaceutics

2022 Volume 19, Issue 9, Page(s) 3358–3366

Abstract: Cocaine is a highly addictive drug that has seen a steady uptrend causing severe health problems worldwide. Currently, there are no approved therapeutics for treating cocaine use disorder; hence, there is an urgent need to identify new medications. ... ...

Abstract	Cocaine is a highly addictive drug that has seen a steady uptrend causing severe health problems worldwide. Currently, there are no approved therapeutics for treating cocaine use disorder; hence, there is an urgent need to identify new medications. Immunopharmacotherapeutics is a promising approach utilizing endogenous antibodies generated through active vaccination, and if properly programmed, can blunt a drug's psychoactive and addictive effects. However, drug vaccine efficacy has largely been limited by the modest levels of antibodies induced. Herein, we explored an adjuvant system consisting of a polyphosphazene macromolecule, specifically poly[di(carboxylatoethylphenoxy)-phosphazene] (PCEP), a biocompatible synthetic polymer that was solicited for improved cocaine conjugate vaccine delivery performance. Our results demonstrated PCEP's superior assembling efficiency with a cocaine hapten as well as with the combined adjuvant CpG oligodeoxynucleotide (ODN). Importantly, this combination led to a higher titer response, balanced immunity, successful sequestering of cocaine in the blood, and a reduction in the drug in the brain. Moreover, a PCEP-cocaine conjugate vaccine was also found to function well via intranasal administration, where its efficacy was demonstrated through the antibody titer, affinity, mucosal IgA production, and a reduction in cocaine's locomotor activity. Overall, a comprehensive evaluation of PCEP integrated within a cocaine vaccine established an advance in the use of synthetic adjuvants in the drugs of abuse vaccine field.
MeSH term(s)	Adjuvants, Immunologic ; Adjuvants, Pharmaceutic/pharmacology ; Cocaine ; Organophosphorus Compounds ; Polymers ; Vaccine Development ; Vaccines, Conjugate
Chemical Substances	Adjuvants, Immunologic ; Adjuvants, Pharmaceutic ; Organophosphorus Compounds ; Polymers ; Vaccines, Conjugate ; poly(phosphazene) ; Cocaine (I5Y540LHVR)
Language	English
Publishing date	2022-08-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2138405-8
ISSN	1543-8392 ; 1543-8384
ISSN (online)	1543-8392
ISSN	1543-8384
DOI	10.1021/acs.molpharmaceut.2c00489
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Article ; Online: Computational discovery of small drug-like compounds as potential inhibitors of SARS-CoV-2 main protease.

Andrianov, Alexander M / Kornoushenko, Yuri V / Karpenko, Anna D / Bosko, Ivan P / Tuzikov, Alexander V

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 15, Page(s) 5779–5791

Abstract: A computational approach to ... ...

Abstract	A computational approach to in
MeSH term(s)	COVID-19 ; Humans ; Molecular Docking Simulation ; Peptide Hydrolases ; Pharmaceutical Preparations ; Protease Inhibitors/pharmacology ; SARS-CoV-2
Chemical Substances	Pharmaceutical Preparations ; Protease Inhibitors ; Peptide Hydrolases (EC 3.4.-)
Keywords	covid19
Language	English
Publishing date	2020-07-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1792989
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Article ; Online: Potential HIV-1 fusion inhibitors mimicking gp41-specific broadly neutralizing antibody 10E8: In silico discovery and prediction of antiviral potency.

Andrianov, Alexander M / Kashyn, Ivan A / Tuzikov, Alexander V

Journal of bioinformatics and computational biology

2018 Volume 16, Issue 2, Page(s) 1840007

Abstract: An integrated computational approach to in silico drug design was used to identify novel HIV-1 fusion inhibitor scaffolds mimicking broadly neutralizing antibody (bNab) 10E8 targeting the membrane proximal external region (MPER) of the HIV-1 gp41 protein. ...

Abstract	An integrated computational approach to in silico drug design was used to identify novel HIV-1 fusion inhibitor scaffolds mimicking broadly neutralizing antibody (bNab) 10E8 targeting the membrane proximal external region (MPER) of the HIV-1 gp41 protein. This computer-based approach included (i) generation of pharmacophore models representing 3D-arrangements of chemical functionalities that make bNAb 10E8 active towards the gp41 MPER segment, (ii) shape and pharmacophore-based identification of the 10E8-mimetic candidates by a web-oriented virtual screening platform pepMMsMIMIC, (iii) high-throughput docking of the identified compounds with the gp41 MPER peptide, and (iv) molecular dynamics simulations of the docked structures followed by binding free energy calculations. As a result, eight hits-able to mimic pharmacophore properties of bNAb 10E8 by specific and effective interactions with the MPER region of the HIV-1 protein gp41 were selected as the most probable 10E8-mimetic candidates. Similar to 10E8, the predicted compounds target the critically important residues of a highly conserved hinge region of the MPER peptide that provides a conformational flexibility necessary for its functioning in cell-virus membrane fusion process. In light of the data obtained, the identified small molecules may present promising HIV-1 fusion inhibitor scaffolds for the design of novel potent antiviral drugs.
MeSH term(s)	Antibodies, Neutralizing/chemistry ; Computational Biology/methods ; Computer Simulation ; Drug Evaluation, Preclinical/methods ; HIV Envelope Protein gp41/chemistry ; HIV Envelope Protein gp41/immunology ; HIV Envelope Protein gp41/metabolism ; HIV Fusion Inhibitors/chemistry ; HIV Fusion Inhibitors/metabolism ; HIV Fusion Inhibitors/pharmacology ; Hydrogen Bonding ; Models, Molecular ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Molecular Mimicry ; Tryptophan/chemistry
Chemical Substances	Antibodies, Neutralizing ; HIV Envelope Protein gp41 ; HIV Fusion Inhibitors ; gp41 protein, Human immunodeficiency virus 1 ; Tryptophan (8DUH1N11BX)
Language	English
Publishing date	2018-01-15
Publishing country	Singapore
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2115015-1
ISSN	1757-6334 ; 0219-7200
ISSN (online)	1757-6334
ISSN	0219-7200
DOI	10.1142/S0219720018400073
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Article ; Online: Repurposing Navitoclax to block SARS-CoV-2 fusion and entry by targeting heptapeptide repeat sequence 1 in S2 protein.

Jiao, Fanke / Andrianov, Alexander M / Wang, Lijue / Furs, Konstantin V / Gonchar, Anna V / Wang, Qian / Xu, Wei / Lu, Lu / Xia, Shuai / Tuzikov, Alexander V / Jiang, Shibo

Journal of medical virology

2023 Volume 95, Issue 10, Page(s) e29145

Abstract: Along with the long pandemic of COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has come the dilemma of emerging viral variants of concern (VOC), particularly Omicron and its subvariants, able to deftly escape immune ... ...

Abstract	Along with the long pandemic of COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has come the dilemma of emerging viral variants of concern (VOC), particularly Omicron and its subvariants, able to deftly escape immune surveillance and the otherwise protective effect of current vaccines and antibody drugs. We previously identified a peptide-based pan-CoV fusion inhibitor, termed as EK1, able to bind the HR1 region in viral spike (S) protein S2 subunit. This effectively blocked formation of the six-helix bundle (6-HB) fusion core and, thus, showed efficacy against all human coronaviruses (HCoVs). EK1 is now in phase 3 clinical trials. However, the peptide drug generally lacks oral availability. Therefore, we herein performed a structure-based virtual screening of the libraries of biologically active molecules and identified nine candidate compounds. One is Navitoclax, an orally active anticancer drug by inhibition of Bcl-2. Like EK1 peptide, it could bind HR1 and block 6-HB formation, efficiently inhibiting fusion and infection of all SARS-CoV-2 variants tested, as well as SARS-CoV and MERS-CoV, with IC
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19 ; Drug Repositioning ; Peptides ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	navitoclax (XKJ5VVK2WD) ; Peptides ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2023-10-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.29145
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Article ; Online: Human immunodeficiency virus-1 gp120 V3 loop for anti-acquired immune deficiency syndrome drug discovery: computer-aided approaches to the problem solving.

Andrianov, Alexander M

Expert opinion on drug discovery

2011 Volume 6, Issue 4, Page(s) 419–435

Abstract: Introduction: The V3 loop on gp120 from HIV-1 is a focus of many research groups involved in anti-AIDS drug development because this region of the protein is the principal target for neutralizing antibodies and determines the preference of the virus for ...

Abstract	Introduction: The V3 loop on gp120 from HIV-1 is a focus of many research groups involved in anti-AIDS drug development because this region of the protein is the principal target for neutralizing antibodies and determines the preference of the virus for T-lymphocytes or primary macrophages. Areas covered: This review summarizes findings related to the 3D structure, conformational mobility, function, antigenicity and immunogenicity of the HIV-1 V3 loop. Particular consideration is given to the V3 loop core sequence Gly-Pro-Gly-Arg/Gln-Ala-Phe, which forms the HIV-1 gp120 immunogenic tip, the role of which has not been completely determined in the virus pathogenesis. New computer-aided approaches for designing potential HIV-1 entry inhibitors are illustrated by a series of examples in which promising basic structures for the V3-based anti-AIDS drug researches have been constructed. Special focus is given to recent studies aimed at defining the structurally conservative V3 sites that may present the HIV-1 weak points most suitable for therapeutic intervention. Finally, the article also discusses how this information can be used to develop novel, potent and broad anti-AIDS agents. Expert opinion: Data on the structure and function of the HIV-1 V3 loop prove convincingly that, in spite of disappointing progress > 20 years, this mysterious site of gp120 (comprising at least three structural motifs recurring in various viral isolates) still remains one of the most attractive targets for the anti-AIDS drug development.
Language	English
Publishing date	2011-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2259618-5
ISSN	1746-045X ; 1746-0441
ISSN (online)	1746-045X
ISSN	1746-0441
DOI	10.1517/17460441.2011.560603
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Article ; Online: Computational identification of novel entry inhibitor scaffolds mimicking primary receptor CD4 of HIV-1 gp120.

Andrianov, Alexander M / Kashyn, Ivan A / Tuzikov, Alexander V

Journal of molecular modeling

2017 Volume 23, Issue 1, Page(s) 18

Abstract: Virtual screening of novel entry inhibitor scaffolds mimicking primary receptor CD4 of HIV-1 gp120 was carried out in conjunction with evaluation of their potential inhibitory activity by molecular modeling. To do this, pharmacophore models presenting ... ...

Abstract	Virtual screening of novel entry inhibitor scaffolds mimicking primary receptor CD4 of HIV-1 gp120 was carried out in conjunction with evaluation of their potential inhibitory activity by molecular modeling. To do this, pharmacophore models presenting different sets of the hotspots of cellular receptor CD4 for its interaction with gp120 were generated. These models were used as the templates for identification of CD4-mimetic candidates by the pepMMsMIMIC screening platform. Complexes of these candidates with gp120 were built by high-throughput ligand docking and their stability was estimated by molecular dynamics simulations and binding free energy calculations. As a result, five top hits that exhibited strong attachment to the two well-conserved hotspots of the gp120 CD4-binding site were selected for the final analysis. In analogy to CD4, the identified compounds make hydrogen bonds with Asp-368
Language	English
Publishing date	2017-01
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1284729-x
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-016-3189-4
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Article ; Online: In silico design and computational evaluation of novel 2-arylaminopyrimidine-based compounds as potential multi-targeted protein kinase inhibitors: application for the native and mutant (T315I) Bcr-Abl tyrosine kinase.

Koroleva, Elena V / Kornoushenko, Yuri V / Karpenko, Anna D / Bosko, Ivan P / Siniutsich, Julia V / Ignatovich, Zhanna V / Andrianov, Alexander M

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 9, Page(s) 4065–4080

Abstract: An integrated computational approach to drug discovery was used to identify novel potential inhibitors of the native and mutant ( ... ...

Abstract	An integrated computational approach to drug discovery was used to identify novel potential inhibitors of the native and mutant (T
MeSH term(s)	Humans ; Adenosine Triphosphate/metabolism ; Antineoplastic Agents/chemistry ; Antineoplastic Agents/pharmacology ; Catalytic Domain ; Computer Simulation ; Drug Design ; Fusion Proteins, bcr-abl/antagonists & inhibitors ; Fusion Proteins, bcr-abl/genetics ; Hydrogen Bonding ; Imatinib Mesylate/pharmacology ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/enzymology ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology ; Ligands ; Machine Learning ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Mutant Proteins/antagonists & inhibitors ; Mutant Proteins/genetics ; Mutation ; Protein Kinase Inhibitors/chemistry ; Protein Kinase Inhibitors/pharmacology ; Pyrimidines/chemistry ; Pyrimidines/pharmacology
Chemical Substances	Adenosine Triphosphate (8L70Q75FXE) ; Antineoplastic Agents ; Fusion Proteins, bcr-abl (EC 2.7.10.2) ; Imatinib Mesylate (8A1O1M485B) ; Ligands ; Mutant Proteins ; nilotinib (F41401512X) ; ponatinib (4340891KFS) ; Protein Kinase Inhibitors ; Pyrimidines
Language	English
Publishing date	2022-04-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2062784
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