1
|
Hossain A, Rahman ME, Faruqe MO, Saif A, Suhi S, Zaman R, Hirad AH, Matin MN, Rabbee MF, Baek KH. Characterization of Plant-Derived Natural Inhibitors of Dipeptidyl Peptidase-4 as Potential Antidiabetic Agents: A Computational Study. Pharmaceutics 2024; 16:483. [PMID: 38675143 PMCID: PMC11053753 DOI: 10.3390/pharmaceutics16040483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/20/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Diabetes, characterized by elevated blood sugar levels, poses significant health and economic risks, correlating with complications like cardiovascular disease, kidney failure, and blindness. Dipeptidyl peptidase-4 (DPP-4), also referred to as T-cell activation antigen CD26 (EC 3.4.14.5.), plays a crucial role in glucose metabolism and immune function. Inhibiting DPP-4 was anticipated as a potential new therapy for diabetes. Therefore, identification of plant-based natural inhibitors of DPP-4 would help in eradicating diabetes worldwide. Here, for the identification of the potential natural inhibitors of DPP-4, we developed a phytochemicals library consisting of over 6000 phytochemicals detected in 81 medicinal plants that exhibited anti-diabetic potency. The library has been docked against the target proteins, where isorhamnetin, Benzyl 5-Amino-5-deoxy-2,3-O-isopropyl-alpha-D-mannofuranoside (DTXSID90724586), and 5-Oxo-7-[4-(trifluoromethyl) phenyl]-4H,6H,7H-[1,2]thiazolo[4,5-b]pyridine 3-carboxylic acid (CHEMBL3446108) showed binding affinities of -8.5, -8.3, and -8.3 kcal/mol, respectively. These compounds exhibiting strong interactions with DPP-4 active sites (Glu205, Glu206, Tyr547, Trp629, Ser630, Tyr662, His740) were identified. ADME/T and bioactivity predictions affirmed their pharmacological safety. Density functional theory calculations assessed stability and reactivity, while molecular dynamics simulations demonstrated persistent stability. Analyzing parameters like RMSD, RG, RMSF, SASA, H-bonds, MM-PBSA, and FEL confirmed stable protein-ligand compound formation. Principal component analysis provided structural variation insights. Our findings suggest that those compounds might be possible candidates for developing novel inhibitors targeting DPP-4 for treating diabetes.
Collapse
Affiliation(s)
- Alomgir Hossain
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (A.H.); (M.E.R.); (R.Z.); (M.N.M.)
| | - Md Ekhtiar Rahman
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (A.H.); (M.E.R.); (R.Z.); (M.N.M.)
| | - Md Omar Faruqe
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh;
| | - Ahmed Saif
- Department of Pharmacy, University of Rajshahi, Rajshahi 6205, Bangladesh;
| | - Suzzada Suhi
- Department of Zoology, University of Rajshahi, Rajshahi 6205, Bangladesh;
| | - Rashed Zaman
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (A.H.); (M.E.R.); (R.Z.); (M.N.M.)
| | - Abdurahman Hajinur Hirad
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
| | - Mohammad Nurul Matin
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (A.H.); (M.E.R.); (R.Z.); (M.N.M.)
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongsangbuk-do, Republic of Korea
| | - Muhammad Fazle Rabbee
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongsangbuk-do, Republic of Korea
| | - Kwang-Hyun Baek
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongsangbuk-do, Republic of Korea
| |
Collapse
|
2
|
Tong JB, Xiao XC, Luo D, Xu HY, Xing YC, Gao P, Liu Y. Discovery of novel BRD4-BD2 inhibitors via in silico approaches: QSAR techniques, molecular docking, and molecular dynamics simulations. Mol Divers 2024; 28:671-692. [PMID: 36773087 DOI: 10.1007/s11030-023-10611-z] [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: 11/27/2022] [Accepted: 01/23/2023] [Indexed: 02/12/2023]
Abstract
Bromodomain-containing protein 4(BRD4) plays an important role in the occurrence and development of various malignant tumors, which has attracted the attention of scientific research institutions and pharmaceutical companies. The structural modification of most currently available BRD4 inhibitors is relatively simple, but the drug effectiveness is limited. Research has found that the inhibition of BD1 may promote the differentiation of oligodendrocyte progenitor cell; however, the inhibition of BD2 will not cause this outcome. Therefore, newly potential drugs which target BRD4-BD2 need further research. Herein, we initially built QSAR models out of 49 compounds using HQSAR, CoMFA, CoMSIA, and Topomer CoMFA technology. All of the models have shown suitable reliabilities (q2 = 0.778, 0.533, 0.640, 0.702, respectively) and predictive abilities (r2pred = 0.716, 0.6289, 0.6153, 0.7968, respectively) for BRD4-BD2 inhibitors. On the basis of QSAR results and the search of the R-group in the topomer search module, we designed 20 new compounds with high activity that showed appropriate docking score and suitable ADMET. Docking studies and MD simulation were carried out to reveal the amino acid residues (Asn351, Cys347, Tyr350, Pro293, and Asp299) at the active site of BRD4-BD2. Free energy calculations and free energy landscapes verified the stable binding results and indicated stable conformations of the complexes. These theoretical studies provide guidance and theoretical basis for designing and developing novel BRD4-BD2 inhibitors.
Collapse
Affiliation(s)
- Jian-Bo Tong
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an,, 710021, People's Republic of China.
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an, 710021, People's Republic of China.
| | - Xue-Chun Xiao
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an,, 710021, People's Republic of China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an, 710021, People's Republic of China
| | - Ding Luo
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, 361005, People's Republic of China
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Hai-Yin Xu
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an,, 710021, People's Republic of China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an, 710021, People's Republic of China
| | - Yi-Chuang Xing
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an,, 710021, People's Republic of China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an, 710021, People's Republic of China
| | - Peng Gao
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an,, 710021, People's Republic of China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an, 710021, People's Republic of China
| | - Yuan Liu
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an,, 710021, People's Republic of China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an, 710021, People's Republic of China
| |
Collapse
|
3
|
Rampogu S, Jung TS, Ha MW, Lee KW. Repurposing and computational design of PARP inhibitors as SARS-CoV-2 inhibitors. Sci Rep 2023; 13:10583. [PMID: 37386052 PMCID: PMC10310815 DOI: 10.1038/s41598-023-36342-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 06/01/2023] [Indexed: 07/01/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a recent pandemic that caused serious global emergency. To identify new and effective therapeutics, we employed a drug repurposing approach. The poly (ADP ribose) polymerase inhibitors were used for this purpose and were repurposed against the main protease (Mpro) target of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2). The results from these studies were used to design compounds using the 'Grow Scaffold' modules available on Discovery Studio v2018. The three designed compounds, olaparib 1826 and olaparib 1885, and rucaparib 184 demonstrated better CDOCKER docking scores for Mpro than their parent compounds. Moreover, the compounds adhered to Lipinski's rule of five and demonstrated a synthetic accessibility score of 3.55, 3.63, and 4.30 for olaparib 1826, olaparib 1885, and rucaparib 184, respectively. The short-range Coulombic and Lennard-Jones potentials also support the potential binding of the modified compounds to Mpro. Therefore, we propose these three compounds as novel SARS-CoV-2 inhibitors.
Collapse
Affiliation(s)
- Shailima Rampogu
- Department of Bio and Medical Big Data (BK4 Program), Division of Life Sciences, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), Jinju, Republic of Korea.
| | - Tae Sung Jung
- Laboratory of Aquatic Animal Diseases, College of Veterinary Medicine, Research Institute of Natural Science, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Min Woo Ha
- Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, Republic of Korea.
| | - Keun Woo Lee
- Department of Bio and Medical Big Data (BK4 Program), Division of Life Sciences, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), Jinju, Republic of Korea.
| |
Collapse
|
4
|
Singh MB, Sharma R, Kumar D, Khanna P, Mansi, Khanna L, Kumar V, Kumari K, Gupta A, Chaudhary P, Kaushik N, Choi EH, Kaushik NK, Singh P. An understanding of coronavirus and exploring the molecular dynamics simulations to find promising candidates against the Mpro of nCoV to combat the COVID-19: A systematic review. J Infect Public Health 2022; 15:1326-1349. [PMID: 36288640 PMCID: PMC9579205 DOI: 10.1016/j.jiph.2022.10.013] [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: 05/02/2022] [Revised: 10/08/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022] Open
Abstract
The first infection case of new coronavirus was reported at the end of 2019 and after then, the cases are reported in all nations across the world in a very short period. Further, the regular news of mutations in the virus has made life restricted with appropriate behavior. To date, a new strain (Omicron and its new subvariant Omicron XE) has brought fear amongst us due to a higher trajectory of increase in the number of cases. The researchers thus started giving attention to this viral infection and discovering drug-like candidates to cure the infections. Finding a drug for any viral infection is not an easy task and takes plenty of time. Therefore, computational chemistry/bioinformatics is followed to get promising molecules against viral infection. Molecular dynamics (MD) simulations are being explored to get drug candidates in a short period. The molecules are screened via molecular docking, which provides preliminary information which can be further verified by molecular dynamics (MD) simulations. To understand the change in structure, MD simulations generated several trajectories such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), hydrogen bonding, and radius of gyration for the main protease (Mpro) of the new coronavirus (nCoV) in the presence of small molecules. Additionally, change in free energy for the formation of complex of Mpro of nCoV with the small molecule can be determined by applying molecular mechanics with generalized born and surface area solvation (MM-GBSA). Thus, the promising molecules can be further explored for clinical trials to combat coronavirus disease-19 (COVID-19).
Collapse
Affiliation(s)
- Madhur Babu Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
| | - Ritika Sharma
- Department of Biochemistry, University of Delhi, New Delhi, India
| | - Durgesh Kumar
- Department of Chemistry, Maitreyi College, University of Delhi, Delhi, India
| | - Pankaj Khanna
- Department of Chemistry, Acharya Narendra Dev College, University of Delhi, New Delhi, India
| | - Mansi
- University School of Basic and Applied Sciences, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Leena Khanna
- University School of Basic and Applied Sciences, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Vinod Kumar
- Special Centre for Nanoscience (SCNS), Jawaharlal Nehru University, New Delhi, India
| | - Kamlesh Kumari
- Department of Zoology, University of Delhi, New Delhi, India
| | - Akanksha Gupta
- Department of Chemistry, Sri Venkateswara College, University of Delhi, New Delhi, India
| | - Preeti Chaudhary
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
| | - Neha Kaushik
- Department of Biotechnology, College of Engineering, The University of Suwon, Hwaseong-si 18323, Republic of Korea.
| | - Eun Ha Choi
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Nagendra Kumar Kaushik
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea.
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India.
| |
Collapse
|
5
|
Islam F, Bibi S, Meem AFK, Islam MM, Rahaman MS, Bepary S, Rahman MM, Rahman MM, Elzaki A, Kajoak S, Osman H, ElSamani M, Khandaker MU, Idris AM, Emran TB. Natural Bioactive Molecules: An Alternative Approach to the Treatment and Control of COVID-19. Int J Mol Sci 2021; 22:12638. [PMID: 34884440 PMCID: PMC8658031 DOI: 10.3390/ijms222312638] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/11/2021] [Accepted: 11/19/2021] [Indexed: 02/07/2023] Open
Abstract
Several coronaviruses (CoVs) have been associated with serious health hazards in recent decades, resulting in the deaths of thousands around the globe. The recent coronavirus pandemic has emphasized the importance of discovering novel and effective antiviral medicines as quickly as possible to prevent more loss of human lives. Positive-sense RNA viruses with group spikes protruding from their surfaces and an abnormally large RNA genome enclose CoVs. CoVs have already been related to a range of respiratory infectious diseases possibly fatal to humans, such as MERS, SARS, and the current COVID-19 outbreak. As a result, effective prevention, treatment, and medications against human coronavirus (HCoV) is urgently needed. In recent years, many natural substances have been discovered with a variety of biological significance, including antiviral properties. Throughout this work, we reviewed a wide range of natural substances that interrupt the life cycles for MERS and SARS, as well as their potential application in the treatment of COVID-19.
Collapse
Affiliation(s)
- Fahadul Islam
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Shabana Bibi
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China;
- International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China
| | - Atkia Farzana Khan Meem
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Md. Mohaimenul Islam
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Md. Saidur Rahaman
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Sristy Bepary
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Md. Mizanur Rahman
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Md. Mominur Rahman
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Amin Elzaki
- Department of Radiological Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.E.); (S.K.); (H.O.); (M.E.)
| | - Samih Kajoak
- Department of Radiological Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.E.); (S.K.); (H.O.); (M.E.)
| | - Hamid Osman
- Department of Radiological Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.E.); (S.K.); (H.O.); (M.E.)
| | - Mohamed ElSamani
- Department of Radiological Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.E.); (S.K.); (H.O.); (M.E.)
| | - Mayeen Uddin Khandaker
- Centre for Applied Physics and Radiation Technologies, School of Engineering and Technology, Sunway University, Bandar Sunway 47500, Selangor, Malaysia;
| | - Abubakr M. Idris
- Department of Chemistry, College of Science, King Khalid University, Abha 62529, Saudi Arabia;
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 62529, Saudi Arabia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| |
Collapse
|
6
|
Poleboyina PK, Rampogu S, Doneti R, Pasha A, Poleboyina SM, Bhanothu S, Pasumarthi D, S D A, Kumbhakar D, Lee KW, Pawar SC. Screening and Identification of Potential iNOS Inhibitors to Curtail Cervical Cancer Progression: an In Silico Drug Repurposing Approach. Appl Biochem Biotechnol 2021; 194:570-586. [PMID: 34705247 DOI: 10.1007/s12010-021-03718-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/08/2021] [Indexed: 11/25/2022]
Abstract
Cervical cancer is the second most common cause of cancer deaths in women worldwide and remains the main reason of mortality among women of reproductive age in developing countries. Nitric oxide is involved in several physiological functions inclusive of inflammatory and immune responses. However, the function of NO in tumor biology is debatable. The inducible NOS (iNOS/NOS2) isoform is the one responsible to maintain the levels of NO, and it exhibits pleotropic effects in various cancers with concentration-dependent pro- and anti-tumor effects. iNOS triggers angiogenesis and endothelial cell migration in tumors by regulating the levels of vascular endothelial growth factor (VEGF). In drug discovery, drug repurposing involves investigations of approved drug candidates to treat various other diseases. In this study, we used anti-cancer drugs and small molecules to target iNOS and identify a potential selective iNOS inhibitor. The structures of ligands were geometrically optimized and energy minimized using Hyperchem software. Molecular docking was performed using Molegro virtual docker, and ligands were selected based on MolDock score, Rerank score, and H-bonding energy. In the study shown, venetoclax compound demonstrated excellent binding affinity to iNOS protein. This compound exhibited the lowest MolDock score and Rerank score with better H-bonding energy to iNOS. The binding efficacy of venetoclax was analyzed by performing molecular docking and molecular dynamic simulations. Multiple parameters were used to analyze the simulation trajectory, like root mean square deviation (RMSD), radius of gyration (Rg), and hydrogen bond interactions. Based on the results, venetoclax emerges to be a promising potential iNOS inhibitor to curtail cervical cancer progression.
Collapse
Affiliation(s)
- Pavan Kumar Poleboyina
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India
| | - Shailima Rampogu
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, South Korea
| | - Ravinder Doneti
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India
| | - Akbar Pasha
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India
| | - Sneha Malleswari Poleboyina
- Department of Pharmaceutical Biotechnology, AU College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, Andhra Pradesh, 530003, India
| | - Shivaji Bhanothu
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India
| | - Deepthi Pasumarthi
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India
| | - Annapurna S D
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India
| | - DivyaVishambhar Kumbhakar
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India
| | - Keun Woo Lee
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, South Korea
| | - Smita C Pawar
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India.
| |
Collapse
|
7
|
Rampogu S, Kim SM, Shaik B, Lee G, Kim JH, Kim GS, Lee KW, Kim MO. Novel Butein Derivatives Repress DDX3 Expression by Inhibiting PI3K/AKT Signaling Pathway in MCF-7 and MDA-MB-231 Cell Lines. Front Oncol 2021; 11:712824. [PMID: 34485148 PMCID: PMC8416463 DOI: 10.3389/fonc.2021.712824] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 06/10/2021] [Indexed: 11/30/2022] Open
Abstract
Background Breast cancer is one of the major causes of mortalities noticed in women globally. DDX3 has emerged as a potent target for several cancers, including breast cancer to which currently there are no reported or approved drugs. Methods To find effective cancer therapeutics, three compounds were computationally designed tweaking the structure of natural compound butein. These compounds were synthesized and evaluated for their anticancer property in MCF-7 and MDA-MB-231 cell lines targeting DDX3. The in silico molecular docking studies have shown that the compounds have occupied the binding site of the human DDX3 target. Furthermore, to investigate the cell viability effect of 3a, 3b, and 3c on MCF-7 and MDA-MB-231 cell lines, the cell lines were treated with different concentrations of compounds for 24 and 48 h and measured using MTT assay. Results The cell viability results showed that the have induced dose dependent suppression of DDX3 expression. Additionally, 3b and 3c have reduced the expression of DDX3 in MCF-7 and MDA-MD-231 cell lines. 3b or 3c treated cell lines increased apoptotic protein expression. Both the compounds have induced the apoptotic cell death by elevated levels of cleaved PARP and cleaved caspase 3 and repression of the anti-apoptosis protein BCL-xL. Additionally, they have demonstrated the G2/M phase cell cycle arrest in both the cell lines. Additionally, 3c decreased PI3K and AKT levels. Conclusions Our results shed light on the anticancer ability of the designed compounds. These compounds can be employed as chemical spaces to design new prospective drug candidates. Additionally, our computational method can be adapted to design new chemical scaffolds as plausible inhibitors.
Collapse
Affiliation(s)
- Shailima Rampogu
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), Jinju, South Korea.,Division of Life Science and Applied Life Science (BK 21 Plus), College of Natural Sciences, Gyeongsang National University, Jinju, South Korea
| | - Seong Min Kim
- Research Institute of Life Science and College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
| | - Baji Shaik
- Department of Chemistry (BK 21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University, Jinju, South Korea
| | - Gihwan Lee
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), Jinju, South Korea
| | - Ju Hyun Kim
- Department of Chemistry (BK 21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University, Jinju, South Korea
| | - Gon Sup Kim
- Research Institute of Life Science and College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
| | - Keun Woo Lee
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), Jinju, South Korea
| | - Myeong Ok Kim
- Division of Life Science and Applied Life Science (BK 21 Plus), College of Natural Sciences, Gyeongsang National University, Jinju, South Korea
| |
Collapse
|