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Otuechere CA, Neupane NP, Adewuyi A, Pathak P, Novak J, Grishina M, Khalilullah H, Jaremko M, Verma A. Green Synthesis of Genistein-Fortified Zinc Ferrite Nanoparticles as a Potent Hepatic Cancer Inhibitor: Validation through Experimental and Computational Studies. Chem Biodivers 2023; 20:e202300719. [PMID: 37312449 DOI: 10.1002/cbdv.202300719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/13/2023] [Accepted: 06/13/2023] [Indexed: 06/15/2023]
Abstract
In hepatic cancer, precancerous nodules account for damage and inflammation in liver cells. Studies have proved that phyto-compounds based on biosynthetic metallic nanoparticles display superior action against hepatic tumors. This study targeted the synthesis of genistein-fortified zinc ferrite nanoparticles (GENP) trailed by anticancer activity assessment against diethylnitrosamine and N-acetyl-2-aminofluorene induced hepatic cancer. The process of nucleation was confirmed by UV/VIS spectrophotometry, X-ray beam diffraction, field-emission scanning electron microscopy, and FT-IR. An in vitro antioxidant assay illustrated that the leaves of Pterocarpus mildbraedii have strong tendency as a reductant and, in the nanoformulation synthesis, as a natural capping agent. A MTT assay confirmed that GENP have a strong selective cytotoxic potential against HepG2 cancer cells. In silico studies of genistein exemplified the binding tendency towards human matrix metalloproteinase comparative to the standard drug marimastat. An in vivo anticancer evaluation showed that GENP effectively inhibit the growth of hepatic cancer by interfering with hepatic and non-hepatic biochemical markers.
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Affiliation(s)
- Chiagoziem A Otuechere
- Department of Biochemistry, Faculty of Basic Medical Sciences, Redeemer's University, 232101, Ede, Nigeria
- Bioorganic and Medicinal Chemistry Research Laboratory, Department of Pharmaceutical Sciences, Sam Higginbottom University of Agriculture, Technology and Sciences, 211007, Prayagraj, India
| | - Netra P Neupane
- Bioorganic and Medicinal Chemistry Research Laboratory, Department of Pharmaceutical Sciences, Sam Higginbottom University of Agriculture, Technology and Sciences, 211007, Prayagraj, India
| | - Adewale Adewuyi
- Department of Chemical Sciences, Faculty of Natural Sciences, Redeemer's University, 232101, Ede, Nigeria
| | - Prateek Pathak
- Bioorganic and Medicinal Chemistry Research Laboratory, Department of Pharmaceutical Sciences, Sam Higginbottom University of Agriculture, Technology and Sciences, 211007, Prayagraj, India
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, 454008, Chelyabinsk, Russia
| | - Jurica Novak
- Department of Biotechnology, University of Rijeka, 51000, Rijeka, Croatia
- Center for Artificial Intelligence and Cybersecurity, University of Rijeka, 51000, Rijeka, Croatia
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, 454008, Chelyabinsk, Russia
| | - Habibullah Khalilullah
- Department of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of Pharmacy, Qassim University, 51911, Unayzah, Saudi Arabia
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Amita Verma
- Bioorganic and Medicinal Chemistry Research Laboratory, Department of Pharmaceutical Sciences, Sam Higginbottom University of Agriculture, Technology and Sciences, 211007, Prayagraj, India
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Novak J, Pathak P, Grishina MA, Potemkin VA. The design of compounds with desirable properties - The anti-HIV case study. J Comput Chem 2023; 44:1016-1030. [PMID: 36533526 DOI: 10.1002/jcc.27061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/14/2022] [Accepted: 12/04/2022] [Indexed: 12/23/2022]
Abstract
Efficacy and safety are among the most desirable characteristics of an ideal drug. The tremendous increase in computing power and the entry of artificial intelligence into the field of computational drug design are accelerating the process of identifying, developing, and optimizing potential drugs. Here, we present novel approach to design new molecules with desired properties. We combined various neural networks and linear regression algorithms to build models for cytotoxicity and anti-HIV activity based on Continual Molecular Interior analysis (CoMIn) and Cinderella's Shoe (CiS) derived molecular descriptors. After validating the reliability of the models, a genetic algorithm was coupled with the Des-Pot Grid algorithm to generate new molecules from a predefined pool of molecular fragments and predict their bioactivity and cytotoxicity. This combination led to the proposal of 16 hit molecules with high anti-HIV activity and low cytotoxicity. The anti-SARS-CoV-2 activity of the hits was predicted.
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Affiliation(s)
- Jurica Novak
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
- Center for Artificial Intelligence and Cybersecurity, University of Rijeka, Rijeka, Croatia
- Scientific and Educational Center "Biomedical Technologies", Higher Medical & Biological School, South Ural State University, Chelyabinsk, Russia
| | - Prateek Pathak
- Laboratory of Computational Modelling of Drugs, Higher Medical & Biological School, South Ural State University, Chelyabinsk, Russia
| | - Maria A Grishina
- Laboratory of Computational Modelling of Drugs, Higher Medical & Biological School, South Ural State University, Chelyabinsk, Russia
| | - Vladimir A Potemkin
- Laboratory of Computational Modelling of Drugs, Higher Medical & Biological School, South Ural State University, Chelyabinsk, Russia
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Novak J, Zykova AR, Potemkin VA, Sharutin VV, Sharutina OK. Platinum(IV) compounds as potential drugs: a quantitative structure-activity relationship study. BIOIMPACTS : BI 2023; 13:373-382. [PMID: 37736338 PMCID: PMC10509740 DOI: 10.34172/bi.2023.24180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/09/2022] [Accepted: 05/10/2022] [Indexed: 09/23/2023]
Abstract
Introduction Machine learning methods, coupled with a tremendous increase in computer power in recent years, are promising tools in modern drug design and drug repurposing. Methods Machine learning predictive models, publicly available at chemosophia.com, were used to predict the bioactivity of recently synthesized platinum(IV) complexes against different kinds of diseases and medical conditions. Two novel QSAR models based on the BiS algorithm are developed and validated, capable to predict activities against the SARS-CoV virus and its RNA dependent RNA polymerase. Results The internal predictive power of the QSAR models was tested by 10-fold cross-validation, giving cross-R2 from 0.863 to 0.903. 38 different activities, ranging from antioxidant, antibacterial, and antiviral activities, to potential anti-inflammatory, anti-arrhythmic and anti-malarial activity were predicted for a series of eighteen platinum(IV) complexes. Conclusion Complexes 1, 3 and 13 have high generalized optimality criteria and are predicted as potential SARS-CoV RNA dependent RNA polymerase inhibitors.
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Affiliation(s)
- Jurica Novak
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
- Center for Artificial Intelligence and Cyber security, University of Rijeka, Rijeka, Croatia
| | - Alena R. Zykova
- Faculty of Chemistry, Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russia
| | | | - Vladimir V. Sharutin
- Faculty of Chemistry, Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russia
| | - Olga K. Sharutina
- Faculty of Chemistry, Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russia
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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] [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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Yadav JP, Grishina M, Shahbaaz M, Mukerjee A, Singh SK, Pathak P. Cucumis melo var. momordica as a potent antidiabetic, antioxidant and possible anticovid alternative: Investigation through experimental and computational methods. Chem Biodivers 2022; 19:e202200200. [PMID: 35950335 DOI: 10.1002/cbdv.202200200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/11/2022] [Indexed: 11/12/2022]
Abstract
Diabetes mellitus is a typical life threatening of disease, which generate due to the dysfunction of β cells of pancreas. In 2014, WHO stated that 422 million people were infected with DM. The current pattern of management of diabetes included synthetic or plant based oral hypoglycemic drugs and insulin but drug resentence is become a very big issues in antidiabetic therapy. Thus, it's very earnest to discover now medication for this disease. Now the days, it is well acknowledged that diabetic patients are more prone towards covid and related complications. Thus, medical practitioners reformed the methodology of prescribing medication for covid infected antidiabetic therapy and encouraging the medication contains dual pharmacological properties. It is also well know that polyphenols specifically hold a significant role in oxidative stress and reduced the severity of many inflammatory diseases. Cucumis melo has rich history as ethano-pharmacological use in Indian subcontinent. The fruit and seed is well known for the treatment of various diseases due to the presence of phenolics. Therefore, in this study, the combined mixture of flower and seeds were used for the extraction of polyphenolic rich extract and tested for antidiabetic activity through the antioxidant and in vivo experiments. The antioxidant potential measurement exhibited that the selected plant has the significant competence to down-regulate oxidative stress (DPPH scavenging IC 50 at 60.7 ±1.05 µg/mL, ABTS IC 50 at 62.15 ± 0.50 µg/mL). Furthermore, the major polyphenolic phyto-compounds derived from the Cucumis melo were used for in silico anticovid activity, docking, and complementarity studies. The anticovid activity prognosis reflected that selected phyto-compounds amentoflavone and vanillic acid have optimal possibility to interact with 3C-like protease and through this moderate anticovid activity can be exhibit. The docking experiments established that the selected compounds have propensity to interact with protein tyrosine phosphatase 1B, 11β-Hydroxysteroid dehydrogenase, superoxide dismutase, glutathione peroxidase, and catalase β-glucuronidase receptor. In vivo experiments showed that 500 mg/kg, Cucumis melo ominously amplified body weight, plasma insulin, high-density lipoprotein levels, and biochemical markers. Furthermore, extract significantly downregulate the blood glucose, total cholesterol, triglycerides, low-density lipoprotein, and very low-density lipoprotein.
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Affiliation(s)
- Jagat Pal Yadav
- UP University: Dr A P J Abdul Kalam Technical University, Faculty of Pharmacy, Kamla Nehru Institute of Management and technology, Sulatnpur, SultanPur, INDIA
| | - Maria Grishina
- South Ural State University (National Research University): Uzno-Ural'skij gosudarstvennyj universitet, Higher Medical and biological School, Lenina, Chelyabinsk, RUSSIAN FEDERATION
| | - Mohd Shahbaaz
- University of the Western Cape, South African Medical Research Council Bioinformatics Unit, Bellville, Cape Town, SOUTH AFRICA
| | - Alok Mukerjee
- Uttar Pradesh Technical University: Dr A P J Abdul Kalam Technical University, Pharmacy, Naini, Allahabad, INDIA
| | - Sunil Kumar Singh
- Uttar Pradesh Technical University: Dr A P J Abdul Kalam Technical University, Pharmacy, Naini, Allahabad, INDIA
| | - Prateek Pathak
- Higher medical and biological school, drug design, prospect lenina, 454008, chelyabinsk, RUSSIAN FEDERATION
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Novak J, Potemkin VA. A new glimpse on the active site of SARS-CoV-2 3CLpro, coupled with drug repurposing study. Mol Divers 2022; 26:2631-2645. [PMID: 35001230 PMCID: PMC8743077 DOI: 10.1007/s11030-021-10355-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/21/2021] [Indexed: 11/03/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is caused by novel severe acute respiratory syndrome coronavirus (SARS-CoV-2). Its main protease, 3C-like protease (3CLpro), is an attractive target for drug design, due to its importance in virus replication. The analysis of the radial distribution function of 159 3CLpro structures reveals a high similarity index. A study of the catalytic pocket of 3CLpro with bound inhibitors reveals that the influence of the inhibitors is local, perturbing dominantly only residues in the active pocket. A machine learning based model with high predictive ability against SARS-CoV-2 3CLpro is designed and validated. The model is used to perform a drug-repurposing study, with the main aim to identify existing drugs with the highest 3CLpro inhibition power. Among antiviral agents, lopinavir, idoxuridine, paritaprevir, and favipiravir showed the highest inhibition potential. Enzyme - ligand interactions as a key ingredient for successful drug design.
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Affiliation(s)
- Jurica Novak
- Higher Medical and Biological School, Laboratory of Computational Modeling of Drugs, South Ural State University, Tchaikovsky Str. 20-A, Chelyabinsk, 454080, Russia.
| | - Vladimir A Potemkin
- Higher Medical and Biological School, Laboratory of Computational Modeling of Drugs, South Ural State University, Tchaikovsky Str. 20-A, Chelyabinsk, 454080, Russia
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7
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Green synthesis of silver nanoformulation of Scindapsus officinalis as potent anticancer and predicted anticovid alternative: Exploration via experimental and computational methods. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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8
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Banerjee S, Katiyar P, Kumar L, Kumar V, Saini SS, Krishnan V, Sircar D, Roy P. Black pepper prevents anemia of inflammation by inhibiting hepcidin over-expression through BMP6-SMAD1/ IL6-STAT3 signaling pathway. Free Radic Biol Med 2021; 168:189-202. [PMID: 33771600 DOI: 10.1016/j.freeradbiomed.2021.03.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/14/2021] [Accepted: 03/17/2021] [Indexed: 01/03/2023]
Abstract
Hepcidin, a circulatory hepatic peptide hormone, is associated with systemic iron homeostasis. Inflammation leads to an increase in hepcidin expression, which dysregulates body iron level. The related disorder, anemia of inflammation, is the second most prevalent anemia-related disorder worldwide. In the present study, we conducted in vitro and in vivo studies to evaluate the effect of black pepper (BP) and its major bioactive alkaloid, piperine, on anemia of inflammation. The initial in vitro study using human hepatocyte cell line, HepG2, confirmed that among different black pepper extracts: methanol (BPME), ethanol (BPEE) and aqueous (BPAE), BPME to be most effective in downregulating transcription of hepcidin gene. Further, BPME and piperine significantly downregulated hepcidin protein expression at 200 μg/ml and 100 μM concentrations, respectively. In the next phase, BPME and piperine were found to significantly attenuate BMP-6 and IL-6 induced hepcidin overexpression by downregulating the increased level of pSMAD1 and pSTAT3 proteins, respectively. For in vivo study, we first subcutaneously injected male BALB/c mice with oil of turpentine, thrice within a period of two weeks, in order to enhance the expression of hepcidin. After that, the intraperitoneal administration of BPME and piperine at 70 and 25 mg/kg body weight, respectively, on alternate days for a period of another two weeks resulted in downregulation of hepcidin overexpression in diseased mice, as confirmed by RT-PCR and immunoblot analysis. The histopathology of liver tissue confirmed increased iron bioavailability in BPME and piperine treated animals. The molecular docking-based interaction studies demonstrated the binding potential of piperine with SMAD1 and STAT3 proteins. The binding patterns supported the proposed inhibition of hepcidin activating proteins. All together, these findings suggest black pepper as a therapeutic candidate for the treatment of anemia of inflammation.
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Affiliation(s)
- Somesh Banerjee
- Molecular Endocrinology Laboratory, Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India.
| | - Parul Katiyar
- Molecular Endocrinology Laboratory, Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India.
| | - Lokesh Kumar
- Molecular Endocrinology Laboratory, Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India.
| | - Vijay Kumar
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India.
| | - Shashank Sagar Saini
- Plant Molecular Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India.
| | - Vengadesan Krishnan
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India.
| | - Debabrata Sircar
- Plant Molecular Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India.
| | - Partha Roy
- Molecular Endocrinology Laboratory, Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India.
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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] [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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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] [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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11
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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] [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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Attenuation of hepatic and breast cancer cells by Polygonatum verticillatum embedded silver nanoparticles. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101863] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Polyphenolic rich extract of Oroxylum indicum alleviate β-glucuronidase activity via down-regulate oxidative stress: Experimental and computational studies. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101804] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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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] [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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15
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Grishina MA, Potemkin VA. Topological Analysis of Electron Density in Large Biomolecular Systems. Curr Drug Discov Technol 2020; 16:437-448. [PMID: 30147011 DOI: 10.2174/1570163815666180821165330] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 08/15/2018] [Accepted: 08/16/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND A great step toward describing the structure of the molecular electron was made in the era of quantum chemical methods. Methods play a very important role in the prediction of molecular properties and in the description of the reactivity of compounds, which cannot be overestimated. There are many works, books, and articles on quantum methods, their applications, and comparisons. At the same time, quantum methods of a high level of theory, which give the most accurate results, are time-consuming, which makes them almost impossible to describe large complex molecular systems, such as macromolecules, enzymes, supramolecular compounds, crystal fragments, and so on. OBJECTIVES To propose an approach that allows real-time estimation of electron density in large systems, such as macromolecules, nanosystems, proteins. METHODS AlteQ approach was applied to the tolopogical analysis of electron density for "substrate - cytochrome" complexes. The approach is based on the use of Slater's type atomic contributions. Parameters of the atomic contributions were found using high resolution X-ray diffraction data for organic and inorganic molecules. Relationships of the parameters with atomic number, ionization potentials and electronegativities were determined. The sufficient quality of the molecular electron structure representation was shown under comparison of AlteQ predicted and observed electron densities. AlteQ algorithm was applied for evaluation of electron structure of "CYP3A4 - substrate" complexes modeled using BiS/MC restricted docking procedure. Topological analysis (similar to Atoms In Molecules (AIM) theory suggested by Richard F.W. Bader) of the AlteQ molecular electron density was carried out for each complex. The determination of (3,-1) bond, (3,+1) ring, (3,+3) cage critical points of electron density in the intermolecular "CYP3A4 - substrate" space was performed. RESULTS Different characteristics such as electron density, Laplacian eigen values, etc. at the critical points were computed. Relationship of pKM (KM is Michaelis constant) with the maximal value of the second Laplacian eigen value of electron density at the critical points and energy of complex formation computed using MM3 force field was determined. CONCLUSION It was shown that significant number of (3,-1) bond critical points are located in the intermolecular space between the enzyme site and groups of substrate atoms eliminating during metabolism processes.
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Affiliation(s)
- Maria A Grishina
- South Ural State University, Laboratory of Computational Modelling of Drugs, Tchaikovsky str. 20-A, Chelyabinsk, Russian Federation
| | - Vladimir A Potemkin
- South Ural State University, Laboratory of Computational Modelling of Drugs, Tchaikovsky str. 20-A, Chelyabinsk, Russian Federation
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Abstract
Background: A principle of complementarity is a well-established concept in chemistry and biology. This concept is based on the overlap of electron clouds of the molecules in question. Materials & methods: In this article, one such approach (an in-house developed quantum free-orbital AlteQ method) was used to evaluate the complementarity of 51 CDK-ligand complexes. Results: A significant universally applicable correlation (adjusted R2 = 0.9749; p < 2.2 × 10-16) relating the product of ligand and enzyme electron densities to the product of distances between the contacting atomic centers and the type of atoms involved in the interaction was found. Conclusion: The terms calculated in this article can provide a good basis for prognosis of bioactivity and scientifically based molecular docking.
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Abstract
AutoDock is one of the most popular receptor-ligand docking simulation programs. It was first released in the early 1990s and is in continuous development and adapted to specific protein targets. AutoDock has been applied to a wide range of biological systems. It has been used not only for protein-ligand docking simulation but also for the prediction of binding affinity with good correlation with experimental binding affinity for several protein systems. The latest version makes use of a semi-empirical force field to evaluate protein-ligand binding affinity and for selecting the lowest energy pose in docking simulation. AutoDock4.2.6 has an arsenal of four search algorithms to carry out docking simulation including simulated annealing, genetic algorithm, and Lamarckian algorithm. In this chapter, we describe a tutorial about how to perform docking with AutoDock4. We focus our simulations on the protein target cyclin-dependent kinase 2.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Val Oliveira Pintro
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.
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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] [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, 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] [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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