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Ivasechko I, Yushyn I, Roszczenko P, Senkiv J, Finiuk N, Lesyk D, Holota S, Czarnomysy R, Klyuchivska O, Khyluk D, Kashchak N, Gzella A, Bielawski K, Bielawska A, Stoika R, Lesyk R. Development of Novel Pyridine-Thiazole Hybrid Molecules as Potential Anticancer Agents. Molecules 2022; 27:molecules27196219. [PMID: 36234755 PMCID: PMC9570594 DOI: 10.3390/molecules27196219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/14/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022] Open
Abstract
Novel pyridine-thiazole hybrid molecules were synthesized and subjected to physico-chemical characterization and screening of their cytotoxic action towards a panel of cell lines derived from different types of tumors (carcinomas of colon, breast, and lung, glioblastoma and leukemia), and normal human keratinocytes, for comparison. High antiproliferative activity of the 3-(2-fluorophenyl)-1-[4-methyl-2-(pyridin-2-ylamino)-thiazol-5-yl]-propenone 3 and 4-(2-{1-(2-fluorophenyl)-3-[4-methyl-2-(pyridin-2-ylamino)-thiazol-5-yl]-3-oxopropylsulfanyl}-acetylamino)-benzoic acid ethyl ester 4 was revealed. The IC50 of the compound 3 in HL-60 cells of the acute human promyelocytic leukemia was 0.57 µM, while in the pseudo-normal human cell lines, the IC50 of this compound was >50 µM, which suggests that the compounds 3 and 4 might be perspective anticancer agents. The detected selectivity of the derivatives 3 and 4 for cancer cell lines inspired us to study the mechanisms of their cytotoxic action. It was shown that preincubation of tumor cells with Fluzaparib (inhibitor of PARP1) reduced the cytotoxic activity of the derivatives 3 and 4 by more than twice. The ability of these compounds to affect DNA nativity and cause changes in nucleus morphology allows for the suggestion that the mechanism of action of the novel pyridine-thiazole derivatives might be related to inducing the genetic instability in tumor cells.
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Affiliation(s)
- Iryna Ivasechko
- Institute of Cell Biology of National Academy of Sciences of Ukraine, 14/16 Drahomanov Str., 79005 Lviv, Ukraine
| | - Ihor Yushyn
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, 79010 Lviv, Ukraine
| | - Piotr Roszczenko
- Department of Biotechnology, Faculty of Pharmacy, Medical University of Bialystok, 15-089 Bialystok, Poland
| | - Julia Senkiv
- Institute of Cell Biology of National Academy of Sciences of Ukraine, 14/16 Drahomanov Str., 79005 Lviv, Ukraine
| | - Nataliya Finiuk
- Institute of Cell Biology of National Academy of Sciences of Ukraine, 14/16 Drahomanov Str., 79005 Lviv, Ukraine
| | - Danylo Lesyk
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, 79010 Lviv, Ukraine
| | - Serhii Holota
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, 79010 Lviv, Ukraine
| | - Robert Czarnomysy
- Department of Synthesis and Technology of Drugs, Faculty of Pharmacy, Medical University of Bialystok, 15-089 Bialystok, Poland
| | - Olga Klyuchivska
- Institute of Cell Biology of National Academy of Sciences of Ukraine, 14/16 Drahomanov Str., 79005 Lviv, Ukraine
| | - Dmytro Khyluk
- Department of Organic Chemistry, Medical University of Lublin, Aleje Racławickie 1, 20-059 Lublin, Poland
| | - Nataliya Kashchak
- Institute of Cell Biology of National Academy of Sciences of Ukraine, 14/16 Drahomanov Str., 79005 Lviv, Ukraine
| | - Andrzej Gzella
- Department of Organic Chemistry, Poznan University of Medical Sciences, Grunwaldzka 6, 60-780 Poznan, Poland
| | - Krzysztof Bielawski
- Department of Synthesis and Technology of Drugs, Faculty of Pharmacy, Medical University of Bialystok, 15-089 Bialystok, Poland
| | - Anna Bielawska
- Department of Biotechnology, Faculty of Pharmacy, Medical University of Bialystok, 15-089 Bialystok, Poland
| | - Rostyslav Stoika
- Institute of Cell Biology of National Academy of Sciences of Ukraine, 14/16 Drahomanov Str., 79005 Lviv, Ukraine
| | - Roman Lesyk
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, 79010 Lviv, Ukraine
- Correspondence: ; Tel.: +380-677038010
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Arshad MF, Alam A, Alshammari AA, Alhazza MB, Alzimam IM, Alam MA, Mustafa G, Ansari MS, Alotaibi AM, Alotaibi AA, Kumar S, Asdaq SMB, Imran M, Deb PK, Venugopala KN, Jomah S. Thiazole: A Versatile Standalone Moiety Contributing to the Development of Various Drugs and Biologically Active Agents. Molecules 2022; 27:molecules27133994. [PMID: 35807236 PMCID: PMC9268695 DOI: 10.3390/molecules27133994] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/05/2022] [Accepted: 06/09/2022] [Indexed: 12/10/2022] Open
Abstract
For many decades, the thiazole moiety has been an important heterocycle in the world of chemistry. The thiazole ring consists of sulfur and nitrogen in such a fashion that the pi (π) electrons are free to move from one bond to other bonds rendering aromatic ring properties. On account of its aromaticity, the ring has many reactive positions where donor–acceptor, nucleophilic, oxidation reactions, etc., may take place. Molecules containing a thiazole ring, when entering physiological systems, behave unpredictably and reset the system differently. These molecules may activate/stop the biochemical pathways and enzymes or stimulate/block the receptors in the biological systems. Therefore, medicinal chemists have been focusing their efforts on thiazole-bearing compounds in order to develop novel therapeutic agents for a variety of pathological conditions. This review attempts to inform the readers on three major classes of thiazole-bearing molecules: Thiazoles as treatment drugs, thiazoles in clinical trials, and thiazoles in preclinical and developmental stages. A compilation of preclinical and developmental thiazole-bearing molecules is presented, focusing on their brief synthetic description and preclinical studies relating to structure-based activity analysis. The authors expect that the current review may succeed in drawing the attention of medicinal chemists to finding new leads, which may later be translated into new drugs.
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Affiliation(s)
- Mohammed F. Arshad
- Department of Research and Scientific Communications, Isthmus Research and Publishing House, U-13, Near Badi Masjid, Pulpehlad Pur, New Delhi 110044, India;
- Correspondence: (M.F.A.); or (S.M.B.A.); (M.I.)
| | - Aftab Alam
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia;
| | - Abdullah Ayed Alshammari
- Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia; (A.A.A.); (M.B.A.); (I.M.A.)
| | - Mohammed Bader Alhazza
- Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia; (A.A.A.); (M.B.A.); (I.M.A.)
| | - Ibrahim Mohammed Alzimam
- Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia; (A.A.A.); (M.B.A.); (I.M.A.)
| | - Md Anish Alam
- Department of Research and Scientific Communications, Isthmus Research and Publishing House, U-13, Near Badi Masjid, Pulpehlad Pur, New Delhi 110044, India;
| | - Gulam Mustafa
- Department of Pharmaceutical Sciences, College of Pharmacy (Al-Dawadmi Campus), Shaqra University, Riyadh 11961, Saudi Arabia;
| | - Md Salahuddin Ansari
- Department of Pharmacy Practice, College of Pharmacy (Al-Dawadmi Campus), Shaqra University, Riyadh 11961, Saudi Arabia;
| | - Abdulelah M. Alotaibi
- Internee, College of Pharmacy (Al-Dawadmi Campus), Shaqra University, Riyadh 11961, Saudi Arabia; (A.M.A.); (A.A.A.)
| | - Abdullah A. Alotaibi
- Internee, College of Pharmacy (Al-Dawadmi Campus), Shaqra University, Riyadh 11961, Saudi Arabia; (A.M.A.); (A.A.A.)
| | - Suresh Kumar
- Drug Regulatory Affair, Department, Pharma Beistand, New Delhi 110017, India;
| | - Syed Mohammed Basheeruddin Asdaq
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Dariyah 13713, Saudi Arabia
- Correspondence: (M.F.A.); or (S.M.B.A.); (M.I.)
| | - Mohd. Imran
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
- Correspondence: (M.F.A.); or (S.M.B.A.); (M.I.)
| | - Pran Kishore Deb
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Philadelphia University, Amman 19392, Jordan;
| | - Katharigatta N. Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia;
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban 4001, South Africa
| | - Shahamah Jomah
- Pharmacy Department, Dr. Sulaiman Al-Habib Medical Group, Riyadh 11372, Saudi Arabia;
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Ndagi U, Abdullahi M, Hamza AN, Magaji MG, Mhlongo NN, Babazhitsu M, Majiya H, Makun HA, Lawal MM. Impact of Drug Repurposing on SARS-Cov-2 Main Protease. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2022; 96. [PMCID: PMC10036164 DOI: 10.1134/s0036024423030299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The recent emergence of the severe acute respiratory disease caused by a novel coronavirus remains a concern posing many challenges to public health and the global economy. The resolved crystal structure of the main protease of SARS-CoV-2 or SCV2 (Mpro) has led to its identification as an attractive target for designing potent antiviral drugs. Herein, we provide a comparative molecular impact of hydroxychloroquine (HCQ), remdesivir, and β-D-N4-Hydroxycytidine (NHC) binding on SCV2 Mpro using various computational approaches like molecular docking and molecular dynamics (MD) simulation. Data analyses showed that HCQ, remdesivir, and NHC binding to SARS-CoV-2 Mpro decrease the protease loop capacity to fluctuate. These binding influences the drugs’ optimum orientation in the conformational space of SCV2 Mpro and produce noticeable steric effects on the interactive residues. An increased hydrogen bond formation was observed in SCV2 Mpro–NHC complex with a decreased receptor residence time during NHC binding. The binding mode of remdesivir to SCV2 Mpro differs from other drugs having van der Waals interaction as the force stabilizing protein–remdesivir complex. Electrostatic interaction dominates in the SCV2 Mpro−HCQ and SCV2 Mpro–NHC. Residue Glu166 was highly involved in the stability of remdesivir and NHC binding at the SCV2 Mpro active site, while Asp187 provides stability for HCQ binding.
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Affiliation(s)
- Umar Ndagi
- Africa Centre of Excellence for Mycotoxin and Food Safety, Federal University of Technology, Minna, Nigeria
| | - Maryam Abdullahi
- Faculty of Pharmaceutical Sciences, Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | - Asmau N. Hamza
- Faculty of Pharmaceutical Sciences, Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | - Mohd G. Magaji
- Faculty of Pharmaceutical Sciences, Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | - Ndumiso N. Mhlongo
- Department of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 4001 Durban, South Africa
| | - Makun Babazhitsu
- Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, Usman Danfodio University, Sokoto, Nigeria
| | - Hussaini Majiya
- Department of Microbiology, Ibrahim Badamasi Babangida University, Lapai, Niger State, Nigeria
| | - Hussaini Anthony Makun
- Africa Centre of Excellence for Mycotoxin and Food Safety, Federal University of Technology, Minna, Nigeria
| | - Monsurat M. Lawal
- Department of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 4001 Durban, South Africa
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Tariq M, Ozbek P, Moin ST. Hydration modulates oxygen channel residues for oxygenation of cysteine dioxygenase: Perspectives from molecular dynamics simulations. J Mol Graph Model 2021; 110:108060. [PMID: 34768230 DOI: 10.1016/j.jmgm.2021.108060] [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] [Received: 07/01/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 11/26/2022]
Abstract
Cysteine dioxygenase (CDO) regulates the concentration of l-cysteine substrate by its oxidation in the body to prevent different diseases, including neurodegenerative and autoimmune diseases. CDO catalyzes the oxidation of thiol group of l-cysteine to l-cysteine sulfinic acid using molecular oxygen. In this study, molecular dynamics simulations were applied to ligand-free CDO, cysteine-bound CDO, and oxygen-bound CDO-cysteine complex which were primarily subjected to the evaluation of their structural and dynamical properties. The simulation data provided significant information not only on the conformational changes of the enzyme after its ligation but also on the co-ligation by sequential binding of l-cysteine and molecular oxygen. It was found that the ligation and co-ligation perturbed the active site region as well as the overall protein dynamics which were analyzed in terms of root mean square deviation, root mean square fluctuation and dynamic cross correlation matrices as well as principal component analysis. Furthermore, oxygen transport pathways were successfully explored by taking various tunnel clusters into account and one of those clusters was given preference based on the throughput value. The bottleneck formed by different amino acid residues was examined to figure out their role in the oxygenation process of the enzyme. The residues forming the tunnel's bottleneck and their dynamics mediated by water molecules were further investigated using radial distribution functions which gave insights into the hydration behavior of these residues. The findings based on the hydration behavior in turn served to explore the water-mediated dynamics of these residues in the modulation of the pathway, including tunnel gating for the oxygen entry and diffusion to the active site, which is essential for the CDO's catalytic function.
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Affiliation(s)
- Muhammad Tariq
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Pemra Ozbek
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, 34722, Turkey.
| | - Syed Tarique Moin
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
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Li HX, Yang WY, Li LP, Zhou H, Li WY, Ma Y, Wang RL. Molecular dynamics study of CDC25B R492L mutant causing the activity decrease of CDC25B. J Mol Graph Model 2021; 109:108030. [PMID: 34509094 DOI: 10.1016/j.jmgm.2021.108030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/01/2021] [Accepted: 09/05/2021] [Indexed: 11/25/2022]
Abstract
Cell division cycle 25B (CDC25B) was responsible for regulating the various stages of cell division in the cell cycle. R492L was one of the common types of CDC25B mutants. Researches showed that compared to CDC25BWT, CDC25BR492L mutant had a ∼100-fold reduction in the rate constant for forming phosphatase intermediate (k2). However, the molecular basis of how the CDC25BR492L mutant influenced the process of binding between CDC25B and CDK2/CyclinA was not yet known. Therefore, the optimizations of three-dimensional structure of the CDC25BWT-CDK2/CyclinA system and the CDC25BR492L-CDK2/CyclinA system were constructed by ZDOCK and RDOCK, and five methods were employed to verify the reasonability of the docking structure. Then the molecular dynamics simulations on the two systems were performed to explore the reason why CDC25BR492L mutant caused the weak interactions between CDC25BR492L and CDK2/CyclinA, respectively. The remote docking site (Arg488-Tyr497) and the second active site (Lys538-Arg544) of CDC25B were observed to have high fluctuations in the CDC25BR492L-CDK2/CyclinA system with post-analysis, where the high fluctuation of these two regions resulted in weak interactions between CD25B and CDK2. In addition, Asp38-Glu42 and Asp206-Asp210 of CDK2 showed the slightly descending fluctuation, and CDK2 revealed an enhanced the self-interaction, which made CDK2 keep a relatively stable state in the CDC25BR492L-CDK2/CyclinA system. Finally, Leu492 of CDC25B was speculated to be the key residue, which had great effects on the binding between CDC25BR492L and CDK2 in the CDC25BR492L-CDK2/CyclinA system. Consequently, overall analyses appeared in this study ultimately offered a helpful understanding of the weak interactions between CDC25BR492L and CDK2.
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Affiliation(s)
- Hao-Xin Li
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Wen-Yu Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, People's Republic of China
| | - Li-Peng Li
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Hui Zhou
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Wei-Ya Li
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Ying Ma
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, People's Republic of China.
| | - Run-Ling Wang
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, People's Republic of China.
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Noorbakhsh A, Askandar RH, Alhagh MS, Farshadfar C, Seyedi SH, Ahmadizad M, Rahimi A, Ardalan N, Koushki EH. Prevention of SARS-CoV-2 Proliferation with a Novel and Potent Main Protease Inhibitor by Docking, ADMET, MM-PBSA, and Molecular Dynamics Simulation. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416521500149] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
COVID-19 is the last disease caused by SARS-CoV-2 associated with a severe immune response and lung damage. The main protease (Mpro) has a vital role in SARS-CoV-2 proliferation. Moreover, humans lack homologous Mpro, which makes the Mpro a suitable drug target for the development of SARS-CoV-2 drugs. The purchasable L5000 library (Selleckchem Inc) includes 99,040 compounds that were used for virtual screening. After molecular docking and ADME studies, we selected a compound (WAY-604395) with a potent binding affinity to the Mpro active site and acceptable ADME properties compared to the reference drug (nelfinavir). Molecular dynamics (MD) simulation outcomes have proved that the Mpro-WAY604395 complex possesses a considerable value of flexibility, stability, compactness and binding energy. Our Molecular Mechanics Poisson–Boltzmann Surface Area (MM-PBSA) calculation demonstrates that WAY-604395 is more potent ([Formula: see text]272.19[Formula: see text]kcal mol[Formula: see text]) in comparison with nelfinavir ([Formula: see text]173.39[Formula: see text]kcal[Formula: see text]mol[Formula: see text]) against SARS-CoV-2 Mpro. In conclusion, we suggest that WAY-604395 has the potential for the treatment of SARS-CoV-2 by inhibition of the Mpro.
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Affiliation(s)
- Akbar Noorbakhsh
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | | | - Mohammad Shakib Alhagh
- School of Life Science, University of Nottingham, Biodiscovery Institute, Nottingham, UK
| | - Chiako Farshadfar
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | - Seyed Hamid Seyedi
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | - Mehran Ahmadizad
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | - Arian Rahimi
- Young Researchers and Elite Club, East Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Noeman Ardalan
- Department of Microbiology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Elnaz Hosseininezhadian Koushki
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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