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Kandagalla S, Grishina M, Novak J, Rimac H, Sharath BS, Potemkin V. AlteQ: a new complementarity principle-centered method for the evaluation of docking poses. J Biomol Struct Dyn 2023; 41:12142-12156. [PMID: 36629044 DOI: 10.1080/07391102.2023.2166120] [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: 09/30/2022] [Accepted: 01/01/2023] [Indexed: 01/12/2023]
Abstract
Molecular docking is the most popular and widely used method for identifying novel molecules against a target of interest. However, docking procedures and their validation are still under intense development. In the present investigation, we evaluate a quantum free-orbital AlteQ method for evaluating docking complexes generated by taking EGFR complexes as an example. The AlteQ method calculates the electron density using Slater's type atomic contributions in the interspace between the receptor and the ligand. Since the interactions are determined by the overlap of electron clouds, they follow the complementarity principle, and an equation can be obtained that describes these interactions. The AlteQ method evaluates the quality of the interaction between the receptor and the ligand, how complementary the interactions are, and due to this, it is used to reject less realistic structures obtained by docking methods. Here, three different equations were used to determine the quality of the interactions in experimental complexes and docked complexes obtained using AutoDock Vina and AutoDock 4.2.6.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shivananda Kandagalla
- Laboratory of Computational Modeling of Drugs, Higher Medical & Biological School, South Ural State University, Chelyabinsk, Russia
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical & Biological School, South Ural State University, Chelyabinsk, Russia
| | - Jurica Novak
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
- Scientific and Educational Center "Biomedical Technologies" School of Medical Biology, South Ural State University, Chelyabinsk, Russia
| | - Hrvoje Rimac
- Department of Medicinal Chemistry, Faculty of Pharmacy & Biochemistry, University of Zagreb, Zagreb, Croatia
| | - B S Sharath
- School of Systems Biomedical Science and Department of Bioinformatics and Life Science, Soongsil University, Seoul, South Korea
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2
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Kandagalla S, Sharath BS, Sherapura A, Grishina M, Potemkin V, Lee J, Ramaswamy G, Prabhakar BT, Hanumanthappa M. A systems biology investigation of curcumin potency against TGF-β-induced EMT signaling in lung cancer. 3 Biotech 2022; 12:306. [PMID: 36276461 PMCID: PMC9526769 DOI: 10.1007/s13205-022-03360-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 03/04/2022] [Accepted: 09/12/2022] [Indexed: 11/01/2022] Open
Abstract
Curcumin (diferuloylmethane) is bioactive phenolic compound which exerts diverse antimetastatic effect. Several studies have reported the antimetastatic effect of curcumin by its ability to modulate the epithelial-to-mesenchymal transition (EMT) process in different cancers, but underlying molecular mechanism is poorly understood. EMT is a highly conserved biological process in which epithelial cells acquire mesenchymal-like characteristics by losing their cell-cell junctions and polarity. As a consequence, deviation in cellular mechanism leads to cancer metastasis and thereby death. In this perspective, we explored the antimetastatic potential and mechanism of curcumin on the EMT process by establishing in vitro EMT model in lungs cancer (A549) cells induced by TGF-β1. Our results showed that curcumin mitigates EMT by regulating the expression of crucial mesenchymal markers such as MMP2, vimentin and N-cadherin. Besides, the transcriptional analysis revealed that the curcumin treatment differentially regulated the expression of 75 genes in NanoString nCounter platform. Further protein-protein interaction network and clusters analysis of differentially expressed genes revealed their involvement in essential biological processes that plays a key role during EMT transition. Altogether, the study provides a comprehensive overview of the antimetastatic potential of curcumin in TGF-β1-induced EMT in lung cancer cells. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03360-7.
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Affiliation(s)
- Shivananda Kandagalla
- Department of PG Studies and Research in Biotechnology and Bioinformatics, Kuvempu University, Jnana Sahyadri, Shankaraghatta, Shivamogga, Karnataka India
- Laboratory of Computational Modeling of Drugs, Higher Medical & Biological School, South Ural State University, 20-A, Tchaikovsky Str., Chelyabinsk, Russia
| | - B. S. Sharath
- Department of PG Studies and Research in Biotechnology and Bioinformatics, Kuvempu University, Jnana Sahyadri, Shankaraghatta, Shivamogga, Karnataka India
- School of Systems Biomedical Science and Department of Bioinformatics and Life Science, Soongsil University, Seoul, South Korea
| | - Ankith Sherapura
- Molecular Biomedicine Laboratory, Postgraduate Department of Studies and Research in Biotechnology, Sahyadri Science College, Kuvempu University, Shivamogga, Karnataka India
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical & Biological School, South Ural State University, 20-A, Tchaikovsky Str., Chelyabinsk, Russia
| | - Vladimir Potemkin
- Laboratory of Computational Modeling of Drugs, Higher Medical & Biological School, South Ural State University, 20-A, Tchaikovsky Str., Chelyabinsk, Russia
| | - Julian Lee
- School of Systems Biomedical Science and Department of Bioinformatics and Life Science, Soongsil University, Seoul, South Korea
| | | | - B. T. Prabhakar
- Molecular Biomedicine Laboratory, Postgraduate Department of Studies and Research in Biotechnology, Sahyadri Science College, Kuvempu University, Shivamogga, Karnataka India
| | - Manjunatha Hanumanthappa
- Department of PG Studies and Research in Biotechnology and Bioinformatics, Kuvempu University, Jnana Sahyadri, Shankaraghatta, Shivamogga, Karnataka India
- Department of Biochemistry, Jnana Bharathi Campus, Bangalore University, Bangalore, Karnataka India
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Kandagalla S, Rimac H, Gurushankar K, Novak J, Grishina M, Potemkin V. Withasomniferol C, a new potential SARS-CoV-2 main protease inhibitor from the Withania somnifera plant proposed by in silico approaches. PeerJ 2022; 10:e13374. [PMID: 35673392 PMCID: PMC9167582 DOI: 10.7717/peerj.13374] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 04/13/2022] [Indexed: 01/13/2023] Open
Abstract
Exploring potent herbal medicine candidates is a promising strategy for combating a pandemic in the present global health crisis. In Ayurveda (a traditional medicine system in India), Withania somnifera (WS) is one of the most important herbs and it has been used for millennia as Rasayana (a type of juice) for its wide-ranging health benefits. WS phytocompounds display a broad spectrum of biological activities (such as antioxidant, anticancer and antimicrobial) modulate detoxifying enzymes, and enhance immunity. Inspired by the numerous biological actions of WS phytocompounds, the present investigation explored the potential of the WS phytocompounds against the SARS-CoV-2 main protease (3CLpro). We selected 11 specific withanolide compounds, such as withaphysalin, withasomniferol, and withafastuosin, through manual literature curation against 3CLpro. A molecular similarity analysis showed their similarity with compounds that have an established inhibitory activity against the SARS-CoV-2. In silico molecular docking and molecular dynamics simulations elucidated withasomniferol C (WS11) as a potential candidate against SARS-CoV-2 3CLpro. Additionally, the present work also presents a new method of validating docking poses using the AlteQ method.
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Affiliation(s)
- Shivananada Kandagalla
- Higher Medical & Biological School, Laboratory of Computational Modeling of Drugs, South Ural State University, Chelyabinsk, Chelyabinsk, Russia
| | - Hrvoje Rimac
- Department of Medicinal Chemistry, University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Krishnamoorthy Gurushankar
- Higher Medical & Biological School, Laboratory of Computational Modeling of Drugs, South Ural State University, Chelyabinsk, Chelyabinsk, Russia,Department of Physics, Kalasalingam Academy of Research and Education, Krishnankoil, Tamilnadu, India
| | - Jurica Novak
- Higher Medical & Biological School, Laboratory of Computational Modeling of Drugs, South Ural State University, Chelyabinsk, Chelyabinsk, Russia
| | - Maria Grishina
- Higher Medical & Biological School, Laboratory of Computational Modeling of Drugs, South Ural State University, Chelyabinsk, Chelyabinsk, Russia
| | - Vladimir Potemkin
- Higher Medical & Biological School, Laboratory of Computational Modeling of Drugs, South Ural State University, Chelyabinsk, Chelyabinsk, Russia
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4
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Kumar S, Gupta Y, Zak SE, Upadhyay C, Sharma N, Herbert AS, Durvasula R, Potemkin V, Dye JM, Poonam, Kempaiah P, Rathi B. A novel compound active against SARS-CoV-2 targeting uridylate-specific endoribonuclease (NendoU/NSP15): in silico and in vitro investigations. RSC Med Chem 2021; 12:1757-1764. [PMID: 34778776 DOI: 10.1039/d1md00202c] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/17/2021] [Indexed: 12/23/2022] Open
Abstract
NendoU (NSP15) is an Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond. Our in-house library was subjected to high throughput virtual screening (HTVS) to identify compounds with potential to inhibit NendoU enzyme, high-rank compounds (those that bound to multiple target structures) were further subjected to 100 nanoseconds MD simulations. Among these, one was found to be bound highly stable within the active site of the NendoU protein structure. Here, we are reporting a derivative of piperazine based '(2S,3S)-3-amino-1-(4-(4-(tert-butyl)benzyl)piperazin-1-yl)-4-phenylbutan-2-ol' (IV) from our in-house libraries having potential efficacy against SARS-CoV-2 in in vitro assays. This compound demonstrated inhibition of viral replication at the same level as Ivermectin, a known SARS-CoV-2 inhibitor, which is not used due to its toxicity at a higher than the currently approved dosage. Compound IV was not toxic to the cell lines up to a 50 μM concentration and exhibited IC50s of 4.97 μM and 8.46 μM in viral entry and spread assay, respectively. Therefore, this novel class of NendoU inhibitor could provide new insights for the development of treatment options for COVID-19.
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Affiliation(s)
- Sumit Kumar
- Department of Chemistry, Miranda House, University of Delhi Delhi India
| | - Yash Gupta
- Division of Infectious Diseases Mayo Clinic, Jacksonville Florida USA
| | - Samantha E Zak
- United States Army Medical Research Institute of Infectious Diseases Fort Detrick MD USA.,The Geneva Foundation 917 Pacific Avenue Tacoma WA USA
| | - Charu Upadhyay
- Department of Chemistry, Miranda House, University of Delhi Delhi India
| | - Neha Sharma
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi India
| | - Andrew S Herbert
- United States Army Medical Research Institute of Infectious Diseases Fort Detrick MD USA
| | - Ravi Durvasula
- Division of Infectious Diseases Mayo Clinic, Jacksonville Florida USA
| | - Vladimir Potemkin
- South Ural State University, Laboratory of Computational Modelling of Drugs 454080 Russia
| | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases Fort Detrick MD USA.,The Geneva Foundation 917 Pacific Avenue Tacoma WA USA
| | - Poonam
- Department of Chemistry, Miranda House, University of Delhi Delhi India
| | - Prakasha Kempaiah
- Division of Infectious Diseases Mayo Clinic, Jacksonville Florida USA
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi India .,South Ural State University, Laboratory of Computational Modelling of Drugs 454080 Russia
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Korina E, Naifert S, Palko N, Grishina M, Potemkin V, Morozov R, Adawy A, Merono R, Avdin V, Schelokov A, Popov V, Bol'shakov O. Probing Adsorption of Dipeptides on Anatase in H 2 O and D 2 O: Thermodynamics and Molecular Geometry. Chemphyschem 2021; 22:2550-2561. [PMID: 34609055 DOI: 10.1002/cphc.202100540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/18/2021] [Revised: 10/05/2021] [Indexed: 01/06/2023]
Abstract
Considering the vast importance of peptide and protein interactions with inorganic surfaces, probing hydrogen bonding during their adsorption on metal oxide surfaces is a relevant task that could shed light on the essential features of their interplay. This work is devoted to studying the dipeptides' adsorption on anatase nanoparticles (ANs) in light and heavy water to reveal differences arising upon the change of the major hydrogen bonding carrier. Thermodynamic study of six native dipeptides' adsorption on ANs in both media shows a strong influence of the solvent on the Gibbs free energy and the effect of side-chain mobile protons on the entropy of the process. The adsorption is endothermic irrespective of the medium and is entropy-driven. Computer simulations of peptide adsorption in both media shows similarity in binding via an amino group and demonstrates structural features of protonated and deuterated peptides in obtained complexes. Calculated peptide- anatase nanoparticle (AN) descriptors indicate surface oxygens as points of peptide-nanoparticle contacts.
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Affiliation(s)
- Elena Korina
- Nanotechnology Education and Research Center, South Ural State University, Chelyabinsk, 454080, Russia
| | - Sergey Naifert
- Nanotechnology Education and Research Center, South Ural State University, Chelyabinsk, 454080, Russia
| | - Nadezhda Palko
- Laboratory of Computational Modelling of Drugs, South Ural State University, Chelyabinsk, 454080, Russia
| | - Maria Grishina
- Laboratory of Computational Modelling of Drugs, South Ural State University, Chelyabinsk, 454080, Russia
| | - Vladimir Potemkin
- Nanotechnology Education and Research Center, South Ural State University, Chelyabinsk, 454080, Russia.,Laboratory of Computational Modelling of Drugs, South Ural State University, Chelyabinsk, 454080, Russia
| | - Roman Morozov
- Laboratory of Computational Modelling of Drugs, South Ural State University, Chelyabinsk, 454080, Russia
| | - Alaa Adawy
- Laboratory of High-Resolution Transmission Electron Microscopy, Institute for Scientific and Technological Resources, University of Oviedo, Oviedo, 33006, Spain
| | - Rafael Merono
- Diffraction Unit, Institute for Scientific and Technological Resources, University of Oviedo, Oviedo, 33006, Spain
| | - Vyacheslav Avdin
- Nanotechnology Education and Research Center, South Ural State University, Chelyabinsk, 454080, Russia
| | - Artyom Schelokov
- Nanotechnology Education and Research Center, South Ural State University, Chelyabinsk, 454080, Russia
| | - Vadim Popov
- Nanotechnology Education and Research Center, South Ural State University, Chelyabinsk, 454080, Russia
| | - Oleg Bol'shakov
- Nanotechnology Education and Research Center, South Ural State University, Chelyabinsk, 454080, Russia.,N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 119991, Russia
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6
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Popovicheva O, Molozhnikova E, Nasonov S, Potemkin V, Penner I, Klemasheva M, Marinaite I, Golobokova L, Vratolis S, Eleftheriadis K, Khodzher T. Industrial and wildfire aerosol pollution over world heritage Lake Baikal. J Environ Sci (China) 2021; 107:49-64. [PMID: 34412787 DOI: 10.1016/j.jes.2021.01.011] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 01/06/2021] [Accepted: 01/10/2021] [Indexed: 06/13/2023]
Abstract
Lake Baikal is the biggest reservoir of fresh water with unique flora and fauna; presently it is negatively affected by climate change, water warming, industrial emissions, shipping, touristic activities, and Siberian forest fires. The assessment of air pollution - related Baikal's ecosystem damage is an unsolved problem. Ship, based expedition exploring the Baikal atmospheric aerosol loading, was performed over the lake area in July 2018. We combine the aerosol near - water and vertical distributions over the Lake Baikal basin with meteorological observations and air mass transportation simulations. Lidar sounding of aerosol fields in the troposphere assesses the atmospheric background in the pristine areas and the pollution during fire-affected periods. Aerosol optical properties (scattering and spectral absorption) converted to the particle number size, black carbon (BC) mass, and Absorption Angstrom Exponent (AAE) provide the inside into aerosol characterization. Transport of industrial emissions from Krasnoyarsk and Irkutsk regions, and wildfire plumes from Republic of Yakutia relates the pollution sources to the increased concentrations of fine particle numbers, PM10 and BC mass over Southern and Northern/Central Baikal, respectively. The highest PM10 and BC are associated to the harbor and touristic areas of intensive shipping and residential biomass burning. Deposition estimates applied to aerosol data exhibit the pollution fluxes to water surface over the whole Baikal area. AAE marks the impact of coal combustion, residential biomass burning, and wildfires indicating the high pollution level of the Lake Baikal ecological system .
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Affiliation(s)
- Olga Popovicheva
- Institute of Nuclear Physics, Lomonosov Moscow State University, Leninskie Gory, 1, 119991 Moscow, Russia.
| | - Elena Molozhnikova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, Irkutsk 664033, Russia
| | - Sergey Nasonov
- Zuev Institute of Atmospheric Optics, Siberian Branch of the Russian Academy of Sciences, Academician Zuev square, 1, Tomsk 634055, Russia
| | - Vladimir Potemkin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, Irkutsk 664033, Russia
| | - Ivan Penner
- Zuev Institute of Atmospheric Optics, Siberian Branch of the Russian Academy of Sciences, Academician Zuev square, 1, Tomsk 634055, Russia
| | - Marina Klemasheva
- Zuev Institute of Atmospheric Optics, Siberian Branch of the Russian Academy of Sciences, Academician Zuev square, 1, Tomsk 634055, Russia
| | - Irina Marinaite
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, Irkutsk 664033, Russia
| | - Ludmila Golobokova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, Irkutsk 664033, Russia
| | - Stergios Vratolis
- Institute of Nuclear&Radiological Sciences&Technology, Energy&Safety, N.C.S.R. "Demokritos", Athens 15310, Greece
| | - Konstantinos Eleftheriadis
- Institute of Nuclear&Radiological Sciences&Technology, Energy&Safety, N.C.S.R. "Demokritos", Athens 15310, Greece
| | - Tamara Khodzher
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, Irkutsk 664033, Russia
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Verma A, Pathak P, Rimac H, Khalilullah H, Kumar V, Grishina M, Potemkin V, Ahmed B. A triterpene glochidon from Phyllanthus debilis: Isolation, computational studies, and antidiabetic activity evaluation. Biocatalysis and Agricultural Biotechnology 2021. [DOI: 10.1016/j.bcab.2021.102138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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8
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Palko N, Grishina M, Potemkin V. Electron Density Analysis of SARS-CoV-2 RNA-Dependent RNA Polymerase Complexes. Molecules 2021; 26:3960. [PMID: 34203564 PMCID: PMC8272208 DOI: 10.3390/molecules26133960] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 11/17/2022] Open
Abstract
The work is devoted to the study of the complementarity of the electronic structures of the ligands and SARS-CoV-2 RNA-dependent RNA polymerase. The research methodology was based on determining of 3D maps of electron densities of complexes using an original quantum free-orbital AlteQ approach. We observed a positive relationship between the parameters of the electronic structure of the enzyme and ligands. A complementarity factor of the enzyme-ligand complexes has been proposed. The console applications of the AlteQ complementarity assessment for Windows and Linux (alteq_map_enzyme_ligand_4_win.exe and alteq_map_enzyme_ligand_4_linux) are available for free at the ChemoSophia webpage.
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Affiliation(s)
- Nadezhda Palko
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, 454080 Chelyabinsk, Russia
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, 454080 Chelyabinsk, Russia
| | - Vladimir Potemkin
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, 454080 Chelyabinsk, Russia
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Novak J, Rimac H, Kandagalla S, Pathak P, Naumovich V, Grishina M, Potemkin V. Proposition of a new allosteric binding site for potential SARS-CoV-2 3CL protease inhibitors by utilizing molecular dynamics simulations and ensemble docking. J Biomol Struct Dyn 2021; 40:9347-9360. [PMID: 34018907 PMCID: PMC8146203 DOI: 10.1080/07391102.2021.1927845] [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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/05/2021] [Indexed: 12/14/2022]
Abstract
The SARS-CoV-2 3CL protease (3CLpro) shows a high similarity with 3CL proteases of other beta-coronaviruses, such as SARS and MERS. It is the main enzyme involved in generating various non-structural proteins that are important for viral replication and is one of the most important proteins responsible for SARS-CoV-2 virulence. In this study, we have conducted an ensemble docking of molecules from the DrugBank database using both the crystallographic structure of the SARS-CoV-2 3CLpro, as well as five conformations obtained after performing a cluster analysis of a 300 ns molecular dynamics (MD) simulation. This procedure elucidated the inappropriateness of the active site for non-covalent inhibitors, but it has also shown that there exists an additional, more favorable, allosteric binding site, which could be a better target for non-covalent inhibitors, as it could prevent dimerization and activation of SARS-CoV-2 3CLpro. Two such examples are radotinib and nilotinib, tyrosine kinase inhibitors already in use for treatment of leukemia and which binding to the newly found allosteric binding site was also confirmed using MD simulations. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jurica Novak
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Hrvoje Rimac
- Department of Medicinal Chemistry, Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Shivananda Kandagalla
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Prateek Pathak
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Vladislav Naumovich
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Vladimir Potemkin
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
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10
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Sharma PP, Kumar S, Kaushik K, Singh A, Singh IK, Grishina M, Pandey KC, Singh P, Potemkin V, Poonam, Singh G, Rathi B. In silico validation of novel inhibitors of malarial aspartyl protease, plasmepsin V and antimalarial efficacy prediction. J Biomol Struct Dyn 2021; 40:8352-8364. [PMID: 33870856 DOI: 10.1080/07391102.2021.1911855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 10/21/2022]
Abstract
Plasmepsin V (Plm V) is an essential aspartic protease required for survival of the malaria parasite, Plasmodium falciparum (Pf). Plm V is required for cleaving the PEXEL motifs of many Pf proteins and its inhibition leads to a knockout effect, indicating its suitability as potential drug target. To decipher new inhibitors of PfPlm V, molecular docking of four HIV-1 protease inhibitors active against PfPlmV was performed on Glide module of Schrödinger suite that supported saquinavir as a lead drug, and therefore, selected as a control. Saquinavir contains an important hydroxyethylamine (HEA) pharmacophore, which was utilized as backbone coupled with piperazine scaffold to build new library of compounds. Newly designed HEA compounds were screened virtually against Plm V. Molecular docking led to a few hits (1 and 3) with higher docking score over the control drug. Notably, compound 1 showed the highest docking score (-11.90 kcal/mol) and XP Gscore (-11.948 kcal/mol). The Prime MMGBSA binding free energy for compound 1 (-60.88 kcal/mol) and 3 (-50.96 kcal/mol) was higher than saquinavir (-37.51 kcal/mol). The binding free energy for the last frame of molecular dynamic simulation supported compound 1 (-92.88 kcal/mol) as potent inhibitor of PfPlm V over saquinavir (-72.77 kcal/mol), and thus, deserves experimental validations in culture and subsequently in animal models.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prem Prakash Sharma
- Department of Biomedical Engineering, Deenbandhu Chhotu Ram, University of Science & Technology, Murthal, Sonepat, Haryana, India.,Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi, India
| | - Sumit Kumar
- Department of Chemistry, Miranda House, University of Delhi, Delhi, India
| | - Kumar Kaushik
- Centre for Fire, Explosives & Environment Safety, Fire Chemistry Group, Delhi, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Indrakant K Singh
- Molecular Biology Research Lab., Department of Zoology, Deshbandhu College, University of Delhi, Delhi, India
| | - Maria Grishina
- Laboratory of Computational Modelling of Drugs, South Ural State University, Russia
| | - Kailash C Pandey
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, New Delhi, India
| | | | - Vladimir Potemkin
- Laboratory of Computational Modelling of Drugs, South Ural State University, Russia
| | - Poonam
- Department of Chemistry, Miranda House, University of Delhi, Delhi, India
| | - Geeta Singh
- Department of Biomedical Engineering, Deenbandhu Chhotu Ram, University of Science & Technology, Murthal, Sonepat, Haryana, India
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi, India.,Laboratory of Computational Modelling of Drugs, South Ural State University, Russia
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11
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Rimac H, Grishina M, Potemkin V. Use of the Complementarity Principle in Docking Procedures: A New Approach for Evaluating the Correctness of Binding Poses. J Chem Inf Model 2021; 61:1801-1813. [PMID: 33797240 PMCID: PMC8154257 DOI: 10.1021/acs.jcim.0c01382] [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] [Indexed: 12/13/2022]
Abstract
![]()
Even
though the first docking procedures were developed almost
40 years ago, they are still under intense development, alongside
with their validation. In this article, we are proposing the use of
the quantum free-orbital AlteQ method in evaluating the correctness
of ligand binding poses and their ranking. The AlteQ method calculates
the electron density in the interspace between the ligand and the
receptor, and since their interactions follow the maximum complementarity
principle, an equation can be obtained, which describes these interactions.
In this way, the AlteQ method evaluates the quality of contacts between
the ligand and the receptor, bypasses the drawbacks of using ligand
RMSD as a measure of docking quality, and can be considered as an
improvement of the “fraction of recovered ligand–receptor
contacts” method. Free Windows and Linux versions of the AlteQ
program for assessing complementarity between the ligand and the receptor
are available for download at www.chemosophia.com.
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Affiliation(s)
- Hrvoje Rimac
- Department of Medicinal Chemistry, University of Zagreb Faculty of Pharmacy and Biochemistry, Ante Kovačića 1, 10000 Zagreb, Croatia
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chaikovskogo 20A, Chelyabinsk 454008, Russia
| | - Vladimir Potemkin
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chaikovskogo 20A, Chelyabinsk 454008, Russia
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12
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Gurushankar K, Rimac H, Potemkin V, Grishina M. Investigation of the newly characterized baimantuoluoamide a and baimantuoluoamide b alkaloids as potential cyclin-dependent kinase 4 (CDK4) inhibitors using molecular docking and molecular dynamics simulations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.129925] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Pathak P, Novak J, Shukla PK, Grishina M, Potemkin V, Verma A. Design, synthesis, antibacterial evaluation, and computational studies of hybrid oxothiazolidin-1,2,4-triazole scaffolds. Arch Pharm (Weinheim) 2021; 354:e2000473. [PMID: 33656194 DOI: 10.1002/ardp.202000473] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/01/2021] [Accepted: 02/04/2021] [Indexed: 11/08/2022]
Abstract
Bacterial infections are a serious threat to human health due to the development of resistance against the presently used antibiotics. The problem of growing and widespread antibiotic resistance is only getting worse with the shortage of new classes of antibiotics, creating a substantial unmet medical need in the treatment of serious bacterial infections. Therefore, in the present work, we report 18 novel hybrid thiazolidine-1,2,4-triazole derivatives as DNA gyrase inhibitors. The derivatives were synthesized by multistep organic synthesis and characterized by spectroscopic methods (1 H and 13 C nuclear magnetic resonance and mass spectroscopy). The derivatives were tested for DNA gyrase inhibition, and the result emphasized that the synthesized derivatives have a tendency to inhibit the function of DNA gyrase. Furthermore, the compounds were also tested for antibacterial activity against three Gram-positive (Bacillus subtilis [NCIM 2063], Bacillus cereus [NCIM 2156], Staphylococcus aureus [NCIM 2079]) and two Gram-negative (Escherichia coli [NCIM 2065], Proteus vulgaris [NCIM 2027]) bacteria. The derivatives showed a significant-to-moderate antibacterial activity with noticeable antibiofilm efficacy. Quantitative structure-activity relationship (QSAR), ADME (absorption, distribution, metabolism, elimination) calculation, molecular docking, radial distribution function, and 2D fingerprinting were also performed to elucidate fundamental structural fragments essential for their bioactivity. These studies suggest that the derivatives 10b and 10n have lead antibacterial properties with significant DNA gyrase inhibitory efficacy, and they can serve as a starting scaffold for the further development of new broad-spectrum antibacterial agents.
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Affiliation(s)
- Prateek Pathak
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Jurica Novak
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Parjanya K Shukla
- Krishnarpit Institute of Pharmacy, Dr. A. P. J. Abdul Kalam Technical University, Prayagraj, Uttar Pradesh, India.,Bioorganic and Medicinal Chemistry Research Laboratory, Department of Pharmaceutical Sciences, Sam Higginbottom University of Agriculture, Technology & Sciences, Prayagraj, Uttar Pradesh, India
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Vladimir Potemkin
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Amita Verma
- Bioorganic and Medicinal Chemistry Research Laboratory, Department of Pharmaceutical Sciences, Sam Higginbottom University of Agriculture, Technology & Sciences, Prayagraj, Uttar Pradesh, India
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14
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Naumovich V, Grishina M, Novak J, Pathak P, Potemkin V, Shahbaaz M, Abdellattif MH. Electronic properties investigation of human dihydrofolate reductase complexes with ligands. J Biomol Struct Dyn 2020; 40:4775-4790. [PMID: 33345753 DOI: 10.1080/07391102.2020.1861985] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Despite the fact that there are already drugs for cancer, they still show strong toxicity to the human organism. That is why it is necessary to establish the factors affecting activity in order to develop new, more effective drugs aimed at tumor cells, minimizing harm to healthy cells. The present research is based on electronic properties calculation of the complexes using AlteQ approach. In the focus of this study are complexes of human dihydrofolate reductase (hDHFR) with a series of known inhibitors bound in the active site. Further, a statistical analysis was performed to establish the relationships between a myriad electronic characteristics and IC50. The change in total volume and the change of own electrons number of hydrogen atoms in their atomic basins are identified as the descriptors correlating the most with the hDHFR inhibition potency. Additionally, two lipophilic parts of protein (Thr56, Ser59, Ile60 and Ile7, Val8, Ala9) were found, which act as a key factor in decreasing bioactivity. The depth analysis of intermolecular interactions showed that the interactions between water molecules and ligand play a crucial role in hDHFR inhibition. Furthermore, the molecular dynamics simulations were used for deeper understanding of the structural inhibition, each for 50 ns time scale in explicit water conditions. Thus, the AlteQ approach made it possible to determine the factors influencing the activity and evaluate them not only qualitatively, but also quantitatively.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vladislav Naumovich
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Jurica Novak
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Prateek Pathak
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Vladimir Potemkin
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Mohd Shahbaaz
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia.,South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, Cape Town, South Africa
| | - Magda H Abdellattif
- Department of Chemistry, College of Science, Deanship of Scientific Research, Taif University, Taif, Saudi Arabia
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15
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Pathak P, Rimac H, Grishina M, Verma A, Potemkin V. Hybrid Quinazoline 1,3,5-Triazines as Epidermal Growth Factor Receptor (EGFR) Inhibitors with Anticancer Activity: Design, Synthesis, and Computational Study. ChemMedChem 2020; 16:822-838. [PMID: 33155373 DOI: 10.1002/cmdc.202000646] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/08/2020] [Indexed: 11/07/2022]
Abstract
We report a series of hybrid quinazoline-1,3,5-triazine derivatives as EGFR inhibitors, which were synthesised and tested by using a variety of in vitro, in silico, and in vivo techniques. The derivatives were found to be active against different cancer cell lines and nontoxic against normal ones, with compounds 7 c, 7 d, 7 e, and 7 j being the most potent ones. The derivatives were also evaluated for angiogenesis inhibition potency in chicken eggs, and molecular docking and dynamics simulation studies were carried out to elucidate the fundamental substituent groups essential for their bioactivity. Additionally, a SAR study of the derivatives was performed for future compound optimisation. These studies suggested that the derivatives have a high affinity towards EGFR with favourable pharmacological properties. The most active compound (7 e) was further evaluated for in vivo anticancer activity against DMBA-induced tumours in female Sprague-Dawley rats as well as its effects on plasma antioxidant status, biotransformation enzymes, and lipid profile. The study suggested that 7 e has lead properties against breast cancer and can serve as a starting compound for further development of anti-EGFR compounds.
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MESH Headings
- 9,10-Dimethyl-1,2-benzanthracene
- Animals
- Antineoplastic Agents/chemical synthesis
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Cell Proliferation/drug effects
- Cell Survival/drug effects
- Dose-Response Relationship, Drug
- Drug Design
- Drug Screening Assays, Antitumor
- ErbB Receptors/antagonists & inhibitors
- ErbB Receptors/metabolism
- Female
- Humans
- Mammary Neoplasms, Experimental/chemically induced
- Mammary Neoplasms, Experimental/drug therapy
- Mammary Neoplasms, Experimental/pathology
- Models, Molecular
- Molecular Structure
- Protein Kinase Inhibitors/chemical synthesis
- Protein Kinase Inhibitors/chemistry
- Protein Kinase Inhibitors/pharmacology
- Quinazolines/chemistry
- Quinazolines/pharmacology
- Rats
- Rats, Sprague-Dawley
- Structure-Activity Relationship
- Triazines/chemistry
- Triazines/pharmacology
- Tumor Cells, Cultured
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Affiliation(s)
- Prateek Pathak
- Laboratory of Computational Modelling of Drugs, South Ural State University, Chaikovskogo 20A, Chelyabinsk, 454008, Russia
| | - Hrvoje Rimac
- Laboratory of Computational Modelling of Drugs, South Ural State University, Chaikovskogo 20A, Chelyabinsk, 454008, Russia
- Department of Medicinal Chemistry, University of Zagreb Faculty of Pharmacy and Biochemistry, Ante Kovacica 1, Zagreb, 10000, Croatia
| | - Maria Grishina
- Laboratory of Computational Modelling of Drugs, South Ural State University, Chaikovskogo 20A, Chelyabinsk, 454008, Russia
| | - Amita Verma
- Bioorganic and Medicinal Chemistry Research Laboratory, Department of Pharmaceutical Sciences, Sam Higginbottom University of Agriculture, Technology & Sciences Naini, Prayagraj, Uttar Pradesh, 211007, India
| | - Vladimir Potemkin
- Laboratory of Computational Modelling of Drugs, South Ural State University, Chaikovskogo 20A, Chelyabinsk, 454008, Russia
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16
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Pathak P, Naumovich V, Grishina M, Potemkin V. The study of EGFR-ligand complex electron property relationship with biological activity. J Biomol Struct Dyn 2020; 40:375-388. [PMID: 32897174 DOI: 10.1080/07391102.2020.1813629] [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] [Indexed: 10/23/2022]
Abstract
The present investigation grounded on estimation of electron properties of the structures of EGFR proteins-ligand complexes using our laboratory-developed methodology AlteQ approach, which describes the molecular electron density of the complex in space for a certain point in three-dimensional coordinates. Briefly, the system embodies molecular electron density as a sum of Slater's type atomic increments of the molecular system. Further, using this methodology, we calculated different electron characteristics of selected EGFR protein-ligand complexes and established the relationship between different electron properties with their experimental pharmacological activity value (pIC50). The study suggested that EGFR inhibitory activity has higher correlation with intermolecular contacts of H with pi-system of aromatic ring between protein and ligands. Therefore, this created model has impact to identify and design potential ligands against EGFR in anticancer drug discovery.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prateek Pathak
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Vladislav Naumovich
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Vladimir Potemkin
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
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17
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Kumar S, Upadhyay C, Bansal M, Grishina M, Chhikara BS, Potemkin V, Rathi B, Poonam. Experimental and Computational Studies of Microwave-Assisted, Facile Ring Opening of Epoxide with Less Reactive Aromatic Amines in Nitromethane. ACS Omega 2020; 5:18746-18757. [PMID: 32775876 PMCID: PMC7408245 DOI: 10.1021/acsomega.0c01760] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/09/2020] [Indexed: 05/05/2023]
Abstract
Nucleophilic ring opening reactions of epoxides with aromatic amines are in the forefront of the synthetic organic chemistry research to build new bioactive scaffolds. Here, convenient, green, and highly efficient regioselective ring opening reactions of sterically hindered (2R,3S)-3-(N-Boc-amino)-1-oxirane-4-phenylbutane with various poorly reactive aromatic amines are accomplished under microwave irradiation in nitromethane. All the reactions effectively implemented for various aromatic amines involve the reuse of nitromethane that supports its dual role as a solvent and catalyst. The corresponding new β-alcohol analogs of hydroxyethylamine (HEA) are isolated in 41-98% yields. The reactions proceed under mild conditions for a broad range of less reactive and sterically hindered aromatic amines. Proton NMR experiments suggest that the nucleophilicity of amines is influenced by nitromethane, which is substantiated by the extensive computational studies. Overall, this methodology elucidates the first-time use of nitromethane as a solvent for the ring opening reactions under microwave conditions involving an equimolar ratio of epoxide and aromatic amine without any catalyst, facile ring opening of complex epoxide by less reactive aromatic amines, low reaction time, less energy consumption, recycling of the solvent, and simple workup procedures.
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Affiliation(s)
- Sumit Kumar
- Department
of Chemistry, Miranda House, University
of Delhi, Delhi 110007, India
| | - Charu Upadhyay
- Department
of Chemistry, Miranda House, University
of Delhi, Delhi 110007, India
| | - Meenakshi Bansal
- Laboratory
for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College University Enclave, University of Delhi, Delhi 110007, India
| | - Maria Grishina
- Laboratory
of Computational Modelling of Drugs, South
Ural State University, Chelyabinsk 454080, Russia
| | - Bhupender S. Chhikara
- Department
of Chemistry, Aditi Mahavidyalaya, University
of Delhi, Bawana, Delhi 110039, India
| | - Vladimir Potemkin
- Laboratory
of Computational Modelling of Drugs, South
Ural State University, Chelyabinsk 454080, Russia
| | - Brijesh Rathi
- Laboratory
for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College University Enclave, University of Delhi, Delhi 110007, India
- Laboratory
of Computational Modelling of Drugs, South
Ural State University, Chelyabinsk 454080, Russia
| | - Poonam
- Department
of Chemistry, Miranda House, University
of Delhi, Delhi 110007, India
- Laboratory
of Computational Modelling of Drugs, South
Ural State University, Chelyabinsk 454080, Russia
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18
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Shahbaaz M, Potemkin V, Bisetty K, Hassan MI, Hussien MA. Classification and functional analyses of putative virulence factors of Mycobacterium tuberculosis: A combined sequence and structure based study. Comput Biol Chem 2020; 87:107270. [PMID: 32438116 DOI: 10.1016/j.compbiolchem.2020.107270] [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: 09/06/2019] [Revised: 04/16/2020] [Accepted: 04/26/2020] [Indexed: 11/17/2022]
Abstract
The emergence of the drug-resistant mechanisms in Mycobacterium tuberculosis poses the biggest challenges to the current therapeutic measures, which necessitates the identification of new drug targets. The Hypothetical Proteins (HPs), a class of functionally uncharacterized proteins, may provide a new class of undiscovered therapeutic targets. The genome of M. tuberculosis contains 1000 HPs with their sequences were analyzed using a variety of bioinformatics tools and the functional annotations were performed. The functions of 662 HPs were successfully predicted and further classified 483 HPs as enzymes, 141 HPs were predicted to be involved in the diverse cellular mechanisms and 38 HPs may function as transporters and carriers proteins. Furthermore, 28 HPs were predicted to be virulent in nature. Amongst them, the HP P95201, HP P9WM79, HP I6WZ30, HP I6 × 9T8, HP P9WKP3, and HP P9WK89 showed the highest virulence scores. Therefore, these proteins were subjected to extensive structure analyses and dynamics of their conformations were investigated using the principles of molecular dynamics simulations, each for a 150 ns time scale. This study provides a deeper understanding of the undiscovered drug targets and the generated outputs will facilitate the process of drug design and discovery against the infection of M. tuberculosis.
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Affiliation(s)
- Mohd Shahbaaz
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute (SANBI), University of the Western Cape, Private Bag X17, Bellville 7535, Cape Town, South Africa; Laboratory of Computational Modeling of Drugs, South Ural State University, 76 Lenin prospekt, 454080 Chelyabinsk, Russia
| | - Vladimir Potemkin
- Laboratory of Computational Modeling of Drugs, South Ural State University, 76 Lenin prospekt, 454080 Chelyabinsk, Russia
| | - Krishna Bisetty
- Department of Chemistry, Durban University of Technology, Durban, 4000, South Africa
| | - Md Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mostafa A Hussien
- Department of Chemistry, Faculty of Science, King Abdulaziz University, P.O. Box 80203 Jeddah 21589, Saudi Arabia; Department of Chemistry, Faculty of Science, Port Said University, Port Said, 42521, Egypt
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19
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Korina E, Naifert S, Morozov R, Potemkin V, Bol'shakov O. Study of Short Peptide Adsorption on Solution Dispersed Inorganic Nanoparticles Using Depletion Method. J Vis Exp 2020. [PMID: 32338648 DOI: 10.3791/60526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Fundamentals of inorganic-organic interactions are critically important in the discovery and development of novel biointerfaces amenable for utilization in biotechnology and medicine. Recent studies indicate that proteins interact with surfaces through limited adsorption sites. Protein fragments such as amino acids and peptides can be used for interaction modeling between complex biological macromolecules and inorganic surfaces. During the last three decades, many valid and sensitive methods have been developed to measure the physical chemistry fundamentals of those interactions: isothermal titration calorimetry (ITC), surface plasmon resonance (SPR), quartz crystal microbalance (QCM), total internal reflection fluorescence (TIRF), and attenuated total reflectance spectroscopy (ATR). The simplest and most affordable technique for the measurement of adsorption is the depletion method, where the change in sorbate concentration (depletion) after contact with solution-dispersed sorbent is calculated and assumed to be adsorbed. Adsorption isotherms based on depletion data provide all basic physicochemical data. However, adsorption from solutions requires longer equilibration times due to kinetic restrictions and sorbents with a high specific surface area, making it almost inapplicable to macroscopic fixed plane surfaces. Moreover, factors such as the instability of sols, nanoparticle aggregates, sorbent crystallinity, nanoparticle size distribution, pH of the solution, and competition for adsorption, should be considered while studying adsorbing peptides. Depletion data isotherm construction provides comprehensive physical chemistry data for literally every soluble sorbate yet remains the most accessible methodology, as it does not require expensive setups. This article describes a basic protocol for the experimental study of peptide adsorption on inorganic oxide and covers all critical points that affect the process.
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Affiliation(s)
- Elena Korina
- Nanotechnology Education and Research Center, South Ural State University
| | - Sergei Naifert
- Nanotechnology Education and Research Center, South Ural State University
| | - Roman Morozov
- Nanotechnology Education and Research Center, South Ural State University
| | - Vladimir Potemkin
- Nanotechnology Education and Research Center, South Ural State University; Laboratory of Computational Modelling of Drugs, South Ural State University
| | - Oleg Bol'shakov
- Nanotechnology Education and Research Center, South Ural State University;
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20
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Palko N, Potemkin V, Grishina M. Theoretical study of the surface structure of anatase nanoparticles: effect on dye adsorption and photovoltaic properties. NEW J CHEM 2020. [DOI: 10.1039/d0nj03213a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The properties of TiO2 can vary greatly, depending on the size and morphology of the particles used.
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Affiliation(s)
- Nadezhda Palko
- South Ural State University
- Laboratory of Computational Modeling of Drugs
- Russia
| | - Vladimir Potemkin
- South Ural State University
- Laboratory of Computational Modeling of Drugs
- Russia
| | - Maria Grishina
- South Ural State University
- Laboratory of Computational Modeling of Drugs
- Russia
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21
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Sharma N, Gupta Y, Bansal M, Singh S, Pathak P, Shahbaaz M, Mathur R, Singh J, Kashif M, Grishina M, Potemkin V, Rajendran V, Poonam, Kempaiah P, Singh AP, Rathi B. Multistage antiplasmodial activity of hydroxyethylamine compounds, in vitro and in vivo evaluations. RSC Adv 2020; 10:35516-35530. [PMID: 35686031 PMCID: PMC9127639 DOI: 10.1039/d0ra03997g] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 08/11/2020] [Indexed: 12/19/2022] Open
Abstract
Malaria, a global threat to the human population, remains a challenge partly due to the fast-growing drug-resistant strains of Plasmodium species. New therapeutics acting against the pathogenic asexual and sexual stages, including liver-stage malarial infection, have now attained more attention in achieving malaria eradication efforts. In this paper, two previously identified potent antiplasmodial hydroxyethylamine (HEA) compounds were investigated for their activity against the malaria parasite's multiple life stages. The compounds exhibited notable activity against the artemisinin-resistant strain of P. falciparum blood-stage culture with 50% inhibitory concentrations (IC50) in the low micromolar range. The compounds' cytotoxicity on HEK293, HepG2 and Huh-7 cells exhibited selective killing activity with IC50 values > 170 μM. The in vivo efficacy was studied in mice infected with P. berghei NK65, which showed a significant reduction in the blood parasite load. Notably, the compounds were active against liver-stage infection, mainly compound 1 with an IC50 value of 1.89 μM. Mice infected with P. berghei sporozoites treated with compound 1 at 50 mg kg−1 dose had markedly reduced liver stage infection. Moreover, both compounds prevented ookinete maturation and affected the developmental progression of gametocytes. Further, systematic in silico studies suggested both the compounds have a high affinity towards plasmepsin II with favorable pharmacological properties. Overall, the findings demonstrated that HEA and piperidine possessing compounds have immense potential in treating malarial infection by acting as multistage inhibitors. Malaria, a global threat to the human population, remains a challenge partly due to the fast-growing drug-resistant strains of Plasmodium species.![]()
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22
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Shahbaaz M, Potemkin V, Grishina M, Bisetty K, Hassan I. The structural basis of acid resistance in Mycobacterium tuberculosis: insights from multiple pH regime molecular dynamics simulations. J Biomol Struct Dyn 2019; 38:4483-4492. [PMID: 31625457 DOI: 10.1080/07391102.2019.1682676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 01/13/2023]
Abstract
The dormant Mycobacterium tuberculosis is evolved to develop the tolerance against the acidification of phagolysosome by the action of gamma interferon. The molecular mechanism responsible for the development of the resistance towards the acidic conditions in M. tuberculosis is not fully understood. Therefore, the current analysis was performed which studies the mechanism of acid tolerance by correlating the alteration in the protonation state of conserved residues in virulent proteins with changes in their folding states. The pH dependencies of proteins were studied using an efficient computational scheme which enables the understanding of their conformational behavior by molecular dynamics (MD) simulations. The adopted methodology involves cyclically updating of the ionization states of titrable residues in the studied proteins with conventional MD steps, which were applied to the newly generated ionization configuration. Significant pH-dependent protein structural stability parameters consistent with the changes of the protonation states of conserved residues were observed. Among the studied proteins, the peptidoglycan binding protein ompATB, carboxylesterase LipF and two-component systems' transcriptional regulator PhoP showed highest structural conservation in the observed acidic pH range throughout the course of MD simulations. The current study provides a better understanding of acid tolerance mechanisms present in M. tuberculosis and can facilitate the drug development strategies against the dormant protein targets.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohd Shahbaaz
- South African National Bioinformatics Institute, University of the Western Cape, Bellville, Cape Town, South Africa.,Laboratory of Computational Modeling of Drugs, South Ural State University, Chelyabinsk, Russia
| | - Vladimir Potemkin
- Laboratory of Computational Modeling of Drugs, South Ural State University, Chelyabinsk, Russia
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, South Ural State University, Chelyabinsk, Russia
| | - Krishna Bisetty
- Department of Chemistry, Durban University of Technology, Durban, South Africa
| | - Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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23
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Pathak P, Shukla PK, Naumovich V, Grishina M, Verma A, Potemkin V. 1,2,4‐Triazole‐conjugated 1,3,4‐thiadiazole hybrid scaffolds: A potent ameliorant of carrageenan‐induced inflammation by lessening proinflammatory mediators. Arch Pharm (Weinheim) 2019; 353:e1900233. [DOI: 10.1002/ardp.201900233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/23/2019] [Accepted: 10/02/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Prateek Pathak
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological SchoolSouth Ural State University Chelyabinsk Russia
| | - Parjanya K. Shukla
- Bioorganic and Medicinal Chemistry Research Laboratory, Department of Pharmaceutical Sciences, Faculty of Health SciencesSam Higginbottom University of Agriculture, Technology and Sciences Allahabad India
- Krishnarpit Institute of PharmacyUttar Pradesh Technical University Allahabad India
| | - Vladislav Naumovich
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological SchoolSouth Ural State University Chelyabinsk Russia
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological SchoolSouth Ural State University Chelyabinsk Russia
| | - Amita Verma
- Bioorganic and Medicinal Chemistry Research Laboratory, Department of Pharmaceutical Sciences, Faculty of Health SciencesSam Higginbottom University of Agriculture, Technology and Sciences Allahabad India
| | - Vladimir Potemkin
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological SchoolSouth Ural State University Chelyabinsk Russia
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Pathak P, Shukla PK, Naumovich V, Grishina M, Potemkin V, Verma A. Silica catalyzed one pot synthesis of hybrid thiazolidin-4-one derivatives as anti-tubercular and anti-inflammatory agent by attenuating COX-2 pathway. SYNTHETIC COMMUN 2019. [DOI: 10.1080/00397911.2019.1643485] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A novel series of a hybrid class of hybrid thiazolidin-4-one derivatives were designed and synthesized through one-pot catalytic synthesis. The reaction was catalyzed in the presence of silica-H2SO4(+6). The derivatives computational ADMET profile was calculated.
The study shows that most active derivatives have optimal logP, higher anti-inflammatory activity score, and poor metabolism at the sight of P450-3A4 and 2D6. The entire series of derivatives were further evaluated for anti-tubercular (against Mycobacterium tuberculosis H37Rv (Resistant
strain)) and anti-inflammatory activity (in-vivo assay using Wistar rat). The result showed that derivatives 4c, 4h, and 4m have significant potency against tested M. tuberculosis. However, derivatives 4i and 4j found significantly active against inflammation.
In vitro COX inhibition assay also supported the result in favor of selectivity and efficacy of derivatives.
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Affiliation(s)
- Prateek Pathak
- Laboratory of Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Parjanya Kumar Shukla
- Bioorganic and Medicinal Chemistry Research Laboratory, Department of Pharmaceutical Sciences, Faculty of Health Sciences, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, India
| | - Vladislav Naumovich
- Laboratory of Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Maria Grishina
- Laboratory of Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Vladimir Potemkin
- Laboratory of Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Amita Verma
- Bioorganic and Medicinal Chemistry Research Laboratory, Department of Pharmaceutical Sciences, Faculty of Health Sciences, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, India
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Pathak P, Naumovich V, Grishina M, Shukla PK, Verma A, Potemkin V. Quinazoline based 1,3,5-triazine derivatives as cancer inhibitors by impeding the phosphorylated RET tyrosine kinase pathway: Design, synthesis, docking, and QSAR study. Arch Pharm (Weinheim) 2019; 352:e1900053. [PMID: 31380598 DOI: 10.1002/ardp.201900053] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 02/20/2019] [Revised: 06/10/2019] [Accepted: 06/18/2019] [Indexed: 11/09/2022]
Abstract
The present research focused on designing a quinazoline skeleton, framed via 1,3,5-triazine derivatives (QBT) through field mapping and alignment studies. The QBT derivatives were synthesized via time- and cost-effective protocol. The 3D-QSAR study, computational physicochemical properties, and ADME calculation of the derivatives were performed to establish the affinity towards the biological system. Molecular docking in the adenosine triphosphate binding site of the RET tyrosine kinase domain (PDB ID: 7IVU) was studied to elucidate vital structural residues necessary for bioactivity. The derivatives were evaluated for anticancer potency against TPC-1 cells (thyroid cancer), MCF-7 cells (breast cancer), and one normal cell line (human foreskin fibroblasts) via 3-(4,5-dimethylthiazol-2-y1)-2,5-diphenyltetrazolium bromide assay followed by an in ovo CAM assay. The entire series of derivatives (8a-o) showed mild to significant anticancer potency against the selected cancer cell lines.
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Affiliation(s)
- Prateek Pathak
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Vladislav Naumovich
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Parjanya Kumar Shukla
- Sam Higginbottom University of Agriculture Technology and Sciences, Allahabad, Uttar Pradesh, India
| | - Amita Verma
- Sam Higginbottom University of Agriculture Technology and Sciences, Allahabad, Uttar Pradesh, India
| | - Vladimir Potemkin
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
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26
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Kumar S, Wu L, Sharma N, Ayushee, Kaushik K, Grishina M, Chhikara BS, Poonam, Potemkin V, Rathi B. Theoretical and experimental studies of an oseltamivir-triazole-based thermoresponsive organogel. RSC Adv 2019; 9:21031-21041. [PMID: 35515532 PMCID: PMC9065751 DOI: 10.1039/c9ra02463h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 04/01/2019] [Accepted: 06/11/2019] [Indexed: 02/01/2023] Open
Abstract
Low-molecular weight organic gelators have been of significant interest in recent years because of their interesting properties and potential applications in sensing technology, biomedicine and drug delivery. Herein, the synthesis, characterization and gelation properties of new oseltamivir conjugates are reported. The oseltamivir-triazole conjugate 1 was synthesized via a click-reaction in a 75% yield. The key features of this conjugate include the presence of amide, flexible ester linkages and a triazole scaffold linking a hydrophobic alkyl chain. The conjugate 1, possessing a long alkyl chain, showed gelation properties in various apolar organic solvents. This gelation behavior was not observed in the case of the deesterified conjugate 2; this indicated the necessity of the alkyl chain for gelation. The gelator 1 showed thermoreversible gelation properties in a range of linear alkane solvents (from n-pentane to n-dodecane). A scanning electron microscopic study suggests that the gelator 1 exists as cross-linked structures, which are self-aggregated in the range of submicrometers, as supported by extensive 1H-NMR studies. The rheological parameters supported the occurrence of a soft gelation process, and the gel formed in n-decane was found to be stiffer than that formed in n-hexane. Computational studies suggested that the gelation behavior was indeed due to micelle formation and dependent on the lipophilicity of solvents.
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Affiliation(s)
- Sumit Kumar
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College University Enclave, University of Delhi Delhi 110007 India .,Department of Chemistry, Miranda House, University of Delhi Delhi 110007 India
| | - Lidong Wu
- Department of Chemistry, Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA.,Key Laboratory of Control of Quality and Safety for Aquatic Products, Ministry of Agriculture, Chinese Academy of Fishery Sciences Beijing 100141 China
| | - Neha Sharma
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College University Enclave, University of Delhi Delhi 110007 India
| | - Ayushee
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College University Enclave, University of Delhi Delhi 110007 India
| | - Kumar Kaushik
- Fire Chemistry Group, Centre for Fire, Explosives & Environment Safety Delhi-110054 India
| | - Maria Grishina
- South Ural State University, Laboratory of Computational Modeling of Drugs 454080 Russia
| | - Bhupendra S Chhikara
- Department of Chemistry, Aditi Mahavidyalaya, University of Delhi Bawana Delhi-110039 India
| | - Poonam
- Department of Chemistry, Miranda House, University of Delhi Delhi 110007 India
| | - Vladimir Potemkin
- South Ural State University, Laboratory of Computational Modeling of Drugs 454080 Russia
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College University Enclave, University of Delhi Delhi 110007 India
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Shchelokov A, Palko N, Potemkin V, Grishina M, Morozov R, Korina E, Uchaev D, Krivtsov I, Bol'shakov O. Adsorption of Native Amino Acids on Nanocrystalline TiO 2: Physical Chemistry, QSPR, and Theoretical Modeling. Langmuir 2019; 35:538-550. [PMID: 30554513 DOI: 10.1021/acs.langmuir.8b02007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The affinity of biomolecules, such as peptides and proteins, with inorganic surfaces, is a fundamental topic in biotechnology and bionanotechnology. Amino acids are often used as "model" bits of peptides or proteins for studying their properties in different environments and/or developing functional surfaces. Despite great demand for knowledge about amino acid interactions with metal oxide surfaces, studies on the issue represent a fragmentary picture. In this paper, we describe amino acid adsorption on nanocrystalline anatase systematically at uniform conditions. Analysis of the Gibbs free adsorption energy indicated how the aliphatic, aromatic, polar, and charged side chain groups affect the binding affinity of the amino acids. Thermodynamic features of the l-amino acid adsorption receive thorough interpretation with calculated molecular descriptors. Theoretical modeling shows that amino acids complex with TiO2 nanoparticles as zwitterions via ammonium group.
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Affiliation(s)
| | | | | | | | | | | | | | - Igor Krivtsov
- Department of Chemical and Environmental Engineering , University of Oviedo , 33006 Oviedo , Spain
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Potemkin V, Potemkin A, Grishina M. Internet Resources for Drug Discovery and Design. Curr Top Med Chem 2019; 18:1955-1975. [DOI: 10.2174/1568026619666181129142127] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/25/2018] [Accepted: 10/12/2018] [Indexed: 11/22/2022]
Abstract
The review describes online resources used for drug discovery and design. Internet resources
can be classified into two classes. The first class of resources accumulates information about drugs,
drug candidates, compounds, and bioassays. This information is a starting point in drug discovery and
design. It is necessary for a training dataset composition. The data found at this step are needed in the
search for the rules predicting a biological activity or recognizing active compounds among other
molecules. The following databases can be used: ChEMBL, different databases of US National Institutes
of Health, DrugBank, PDBind-CN Database, RCSB Protein Data Bank (PDB), BRENDA, etc.
The second class of Internet resources includes web-portals performing online computations for drug
discovery and design. The web-portals perform: 1) modelling of molecular structure such as geometry
optimization and molecular docking; 2) online computations of various descriptors, physical-chemical
and ADMET properties influencing the bioprocesses occurring in a living organism along the road of
the drug therapeutic action; 3) quantitative structure-activity relationship (QSAR) and quantitative
structure-property relationship (QSPR) studies; 4) prognosis of bioactivities of compounds; 5) design of
new drug candidates. These are, for example, ChemAxon, ACD/ I-lab, Mcule, OCHEM, eADMET,
ChemoSophia, DockingServer, 1-click Docking, MDWeb, DockingServer, ZDOCK, etc. The role of
docking online resources for modeling of “ligand-receptor” complexes, prognosis of bioactivities, and
drug design is discussed. The review highlights the possibilities of Internet resources for a study of a
drug action at the most important stages. A detailed assessment of the advantages of the reviewed Internet
resources is done.
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Affiliation(s)
- Vladimir Potemkin
- Laboratory of Computational Modeling of Drugs, South Ural State University, Pr. Lenina, 76, Chelyabinsk 454080, Russian Federation
| | | | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, South Ural State University, Pr. Lenina, 76, Chelyabinsk 454080, Russian Federation
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Poonam P, Kumari P, Grishina M, Potemkin V, Verma A, Rathi B. Oxygen mediated highly efficient cobalt(ii) porphyrin-catalyzed reduction of functional chromones: experimental and computational studies. NEW J CHEM 2019. [DOI: 10.1039/c9nj00266a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The highly efficient oxygen mediated reduction of functional chromones with sodium borohydride (NaBH4) catalyzed by cobalt(ii) porphyrins afforded biologically active chroman-4-ols as the reduction products in 80–98% yields.
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Affiliation(s)
- Poonam Poonam
- Department of Chemistry
- Miranda House
- University of Delhi
- Delhi-110007
- India
| | - Pratibha Kumari
- Department of Chemistry
- Deshbandhu College
- University of Delhi
- Delhi-110007
- India
| | - Maria Grishina
- South Ural State University
- Laboratory of Computational Modeling of Drugs
- Russia
| | - Vladimir Potemkin
- South Ural State University
- Laboratory of Computational Modeling of Drugs
- Russia
| | - Abhishek Verma
- Laboratory for Translational Chemistry and Drug Discovery
- Department of Chemistry
- Hansraj College
- University of Delhi
- Delhi-110007
| | - Brijesh Rathi
- South Ural State University
- Laboratory of Computational Modeling of Drugs
- Russia
- Laboratory for Translational Chemistry and Drug Discovery
- Department of Chemistry
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Abstract
Various techniques for rational drug design are presented in the paper. The methods are based
on a substitution of antipharmacophore atoms of the molecules of training dataset by new atoms and/or
group of atoms increasing the atomic bioactivity increments obtained from an SAR study. Furthermore, a
design methodology based on the genetic algorithm DesPot for discrete optimization and generation of
new drug candidate structures is described. Additionally, wide spectra of SAR approaches (3D/4D QSAR
interior and exterior-based methods – BiS, CiS, ConGO, CoMIn, high-quality docking method - ReDock)
using MERA force field and/or AlteQ quantum chemical method for correct prognosis of bioactivity and
the bioactive probability have been described. The design methods are implemented at
www.chemosophia.com web-site for online computational services.
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Affiliation(s)
- Vladimir Potemkin
- South Ural State University, 20-A, Tchaikovsky Str., Chelyabinsk 454080, Russian Federation
| | - Maria Grishina
- South Ural State University, 20-A, Tchaikovsky Str., Chelyabinsk 454080, Russian Federation
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31
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Kumar Singh A, Rajendran V, Singh S, Kumar P, Kumar Y, Singh A, Miller W, Potemkin V, Poonam, Grishina M, Gupta N, Kempaiah P, Durvasula R, Singh BK, Dunn BM, Rathi B. Antiplasmodial activity of hydroxyethylamine analogs: Synthesis, biological activity and structure activity relationship of plasmepsin inhibitors. Bioorg Med Chem 2018; 26:3837-3844. [PMID: 29983285 DOI: 10.1016/j.bmc.2018.06.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 03/09/2018] [Revised: 06/26/2018] [Accepted: 06/28/2018] [Indexed: 01/08/2023]
Abstract
Malaria, particularly in endemic countries remains a threat to the human health and is the leading the cause of mortality in the tropical and sub-tropical areas. Herein, we explored new C2 symmetric hydroxyethylamine analogs as the potential inhibitors of Plasmodium falciparum (P. falciparum; 3D7) in in-vitro cultures. All the listed compounds were also evaluated against crucial drug targets, plasmepsin II (Plm II) and IV (Plm IV), enzymes found in the digestive vacuole of the P. falciparum. Analog 10f showed inhibitory activities against both the enzymes Plm II and Plm IV (Ki, 1.93 ± 0.29 µM for Plm II; Ki, 1.99 ± 0.05 µM for Plm IV). Among all these analogs, compounds 10g selectively inhibited the activity of Plm IV (Ki, 0.84 ± 0.08 µM). In the in vitro screening assay, the growth inhibition of P. falciparum by both the analogs (IC50, 2.27 ± 0.95 µM for 10f; IC50, 3.11 ± 0.65 µM for 10g) displayed marked killing effect. A significant growth inhibition of the P. falciparum was displayed by analog 12c with IC50 value of 1.35 ± 0.85 µM, however, it did not show inhibitory activity against either Plms. The hemolytic assay suggested that the active compounds selectively inhibit the growth of the parasite. Further, potent analogs (10f and 12c) were evaluated for their cytotoxicity towards mammalian HepG2 and vero cells. The selectivity index (SI) values were noticed greater than 10 for both the analogs that suggested their poor toxicity. The present study indicates these analogs as putative lead structures and could serve as crucial for the development of new drug molecules.
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Affiliation(s)
- Amit Kumar Singh
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Vinoth Rajendran
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Snigdha Singh
- Department of Chemistry, University of Delhi, Delhi 110007, India; Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi 110007, India
| | - Prashant Kumar
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Yogesh Kumar
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi 110007, India
| | - Archana Singh
- Department of Botany, Hansraj College University Enclave, University of Delhi, Delhi 110007, India
| | - Whelton Miller
- Department of Chemistry & Physics, Lincoln University, Lincoln University, PA 19352, USA; Department of Chemical & Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Vladimir Potemkin
- South Ural State University, Laboratory of Computational Modeling of Drugs, 454080, Russia
| | - Poonam
- South Ural State University, Laboratory of Computational Modeling of Drugs, 454080, Russia; Department of Chemistry, Miranda House University Enclave, University of Delhi, Delhi 110007 India
| | - Maria Grishina
- South Ural State University, Laboratory of Computational Modeling of Drugs, 454080, Russia
| | - Nikesh Gupta
- Special Centre for Nanosciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Prakasha Kempaiah
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Ravi Durvasula
- Department of Medicine, Loyola University Stritch School of Medicine, Maywood, IL 60153, USA
| | | | - Ben M Dunn
- Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, P.O. Box 100245, Gainesville, FL, USA
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi 110007, India; South Ural State University, Laboratory of Computational Modeling of Drugs, 454080, Russia.
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Potemkin V, Bolshakov O, Safiullin A, Potemkin A, Grishina M. Design and theoretical study of D–A–pi–A' organic sensitizers with [1,2,5]oxa-, thia- or selenadiazoloazine fragment. ARKIVOC 2017. [DOI: 10.24820/ark.5550190.p010.228] [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: 11/23/2022] Open
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Grishina M, Bolshakov O, Potemkin A, Potemkin V. Theoretical investigation of electron structure and surface morphology of titanium dioxide anatase nano-particles. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Sushko I, Novotarskyi S, Körner R, Pandey AK, Rupp M, Teetz W, Brandmaier S, Abdelaziz A, Prokopenko VV, Tanchuk VY, Todeschini R, Varnek A, Marcou G, Ertl P, Potemkin V, Grishina M, Gasteiger J, Schwab C, Baskin II, Palyulin VA, Radchenko EV, Welsh WJ, Kholodovych V, Chekmarev D, Cherkasov A, Aires-de-Sousa J, Zhang QY, Bender A, Nigsch F, Patiny L, Williams A, Tkachenko V, Tetko IV. Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. J Comput Aided Mol Des 2011; 25:533-54. [PMID: 21660515 PMCID: PMC3131510 DOI: 10.1007/s10822-011-9440-2] [Citation(s) in RCA: 351] [Impact Index Per Article: 27.0] [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: 02/22/2011] [Accepted: 05/24/2011] [Indexed: 11/25/2022]
Abstract
The Online Chemical Modeling Environment is a web-based platform that aims to automate and simplify the typical steps required for QSAR modeling. The platform consists of two major subsystems: the database of experimental measurements and the modeling framework. A user-contributed database contains a set of tools for easy input, search and modification of thousands of records. The OCHEM database is based on the wiki principle and focuses primarily on the quality and verifiability of the data. The database is tightly integrated with the modeling framework, which supports all the steps required to create a predictive model: data search, calculation and selection of a vast variety of molecular descriptors, application of machine learning methods, validation, analysis of the model and assessment of the applicability domain. As compared to other similar systems, OCHEM is not intended to re-implement the existing tools or models but rather to invite the original authors to contribute their results, make them publicly available, share them with other users and to become members of the growing research community. Our intention is to make OCHEM a widely used platform to perform the QSPR/QSAR studies online and share it with other users on the Web. The ultimate goal of OCHEM is collecting all possible chemoinformatics tools within one simple, reliable and user-friendly resource. The OCHEM is free for web users and it is available online at http://www.ochem.eu.
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Affiliation(s)
- Iurii Sushko
- eADMET GmbH, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
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Potemkin V, Grishina M. Principles for 3D/4D QSAR classification of drugs. Drug Discov Today 2008; 13:952-9. [PMID: 18721896 DOI: 10.1016/j.drudis.2008.07.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Revised: 06/26/2008] [Accepted: 07/21/2008] [Indexed: 11/27/2022]
Abstract
The principles for the 3D/4D classification of drugs are introduced in this article. Based on these principles, new techniques for the reconstruction of complementary selfconsistent receptor fields for the classification of drugs, taking into account their multitautomeric and multiconformational states, are created. The series of examples of classification of drugs by their activity (active or nonactive), by their mechanisms of action, by their target and binding site and by the most important stages of their action are given. Prospects for rational drug design are highlighted.
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Affiliation(s)
- Vladimir Potemkin
- Chelyabinsk State University, Br. Kashirinych 129, Chelyabinsk 454021, Russian Federation.
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Tsirelson V, Stash A, Zhurova E, Zhurov V, Pinkerton AA, Zavodnik V, Shutalev A, Gurskaya G, Rykounov A, Potemkin V. Electron-density properties of the functionally-substituted hydropyrimidines. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305081997] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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