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Ja'afaru SC, Uzairu A, Hossain S, Ullah MH, Sallau MS, Ndukwe GI, Ibrahim MT, Bayil I, Moin AT. Computer-aided discovery of novel SmDHODH inhibitors for schistosomiasis therapy: Ligand-based drug design, molecular docking, molecular dynamic simulations, drug-likeness, and ADMET studies. PLoS Negl Trop Dis 2024; 18:e0012453. [PMID: 39264908 PMCID: PMC11392272 DOI: 10.1371/journal.pntd.0012453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 08/13/2024] [Indexed: 09/14/2024] Open
Abstract
Schistosomiasis, also known as bilharzia or snail fever, is a tropical parasitic disease resulting from flatworms of the Schistosoma genus. This often overlooked disease has significant impacts in affected regions, causing enduring morbidity, hindering child development, reducing productivity, and creating economic burdens. Praziquantel (PZQ) is currently the only treatment option for schistosomiasis. Given the potential rise of drug resistance and the limited treatment choices available, there is a need to develop more effective inhibitors for this neglected tropical disease (NTD). In view of this, quantitative structure-activity relationship studies (QSAR), molecular docking, molecular dynamics simulations, drug-likeness, and ADMET predictions were applied to 31 inhibitors of Schistosoma mansoni Dihydroorotate dehydrogenase (SmDHODH). The designed QSAR model demonstrated robust statistical parameters including an R2 of 0.911, R2adj of 0.890, Q2cv of 0.686, R2pred of 0.807, and cR2p of 0.825, confirming its robustness. Compound 26, identified as the most active derivative, emerged as a lead candidate for new potential inhibitors through ligand-based drug design. Subsequently, 12 novel compounds (26A-26L) were designed with enhanced inhibition activity and binding affinity. Molecular docking studies revealed strong and stable interactions, including hydrogen bonding and hydrophobic interactions, between the designed compounds and the target receptor. Molecular dynamics simulations over 100 nanoseconds and MM-PBSA free binding energy (ΔGbind) calculations validated the stability of the two best-designed molecules (26A and 26L). Furthermore, drug-likeness and ADMET prediction analyses affirmed the potential of these designed compounds, suggesting their promise as innovative agents for treating schistosomiasis.
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Affiliation(s)
- Saudatu Chinade Ja'afaru
- Department of Chemistry, Ahmadu Bello University, Zaria, Nigeria
- Department of Chemistry, Aliko Dangote University of Science and Technology, Wudil, Nigeria
| | - Adamu Uzairu
- Department of Chemistry, Ahmadu Bello University, Zaria, Nigeria
| | - Sharika Hossain
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Mohammad Hamid Ullah
- Department of Pharmacy, University of Cyberjaya Medical Science, Cyberjaya Selangor, Malaysia
| | | | | | | | - Imren Bayil
- Department of Bioinformatics and Computational Biology, Gaziantep University, Gaziantep, Turkey
| | - Abu Tayab Moin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
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Kubo AI, Uzairu A, Babalola IT, Ibrahim MT, Umar AB. QSAR, molecular docking, and pharmacokinetic analysis of thiosemicarbazone-indole compounds targeting prostate cancer cells. J Taibah Univ Med Sci 2024; 19:823-834. [PMID: 39228962 PMCID: PMC11369465 DOI: 10.1016/j.jtumed.2024.07.004] [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: 05/23/2023] [Revised: 05/23/2024] [Accepted: 07/24/2024] [Indexed: 09/05/2024] Open
Abstract
Objectives By 2030, prostate cancer is estimated to account for 1.7 million new cases and 499,000 deaths. The objectives of this research were to create a model revealing the activity of thiosemicarbazone-indole compounds as anticancer agents against the PC3 cell line; perform docking analysis between the compounds and the target enzyme; and predict the pharmacokinetics and drug-likeness of the compounds under investigation. Methods The quantitative structureactivity relationship (QSAR) method was used to build the model; molecular docking between the compounds and the target enzyme was performed; and the drug-likeness and pharmacokinetics of the inhibiting compounds was examined. Results The genetic function algorithm-multilinear regression approach was used for building the QSAR model. Build model 1 had the best performance, with R2 (coefficient of determination) = 0.972517, Radj (adjusted R-squared) = 0.964665, (CRp2) = 0.780922, and LOF (leave-one-out cross-validation) = 0.076524, demonstrated strongly indicated by the molecular descriptors. SHBd, SsCH3, JGI2, and RDF60P were highly dependent on proliferative activity. Compounds ID 7 and 22 had the potential to act as androgen receptor inhibitors, as suggested by molecular docking studies between the drugs and their target enzymes. Compounds ID 7 and 22 exhibited binding scores of -8.5 kcal/mol and -8.8 kcal/mol, respectively. The approved maximum medication molecules for oral bioavailability included the molecules with IDs 7 and 22. Conclusion This research provides valuable insights into the relationships among molecular descriptors, potential inhibitors, and pharmacokinetic properties in the treatment of PC3. These findings may contribute to the understanding and potential development of new therapeutic options for prostate cancer patients.
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Affiliation(s)
- Abdulrahman Ibrahim Kubo
- Department of Chemistry, Faculty of Science, Yobe State University, Damaturu, Nigeria
- Department of Pure and Applied Chemistry, Faculty of Science, Adamawa State University, Mubi, Nigeria
| | - Adamu Uzairu
- Department of Chemistry, Faculty of Physical Science, Ahmadu Bello University, Zaria, Nigeria
| | | | - Muhammad Tukur Ibrahim
- Department of Chemistry, Faculty of Physical Science, Ahmadu Bello University, Zaria, Nigeria
| | - Abdullahi Bello Umar
- Department of Chemistry, Faculty of Physical Science, Ahmadu Bello University, Zaria, Nigeria
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Ja’afaru SC, Uzairu A, Bayil I, Sallau MS, Ndukwe GI, Ibrahim MT, Moin AT, Mollah AKMM, Absar N. Unveiling potent inhibitors for schistosomiasis through ligand-based drug design, molecular docking, molecular dynamics simulations and pharmacokinetics predictions. PLoS One 2024; 19:e0302390. [PMID: 38923997 PMCID: PMC11207139 DOI: 10.1371/journal.pone.0302390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/02/2024] [Indexed: 06/28/2024] Open
Abstract
Schistosomiasis is a neglected tropical disease which imposes a considerable and enduring impact on affected regions, leading to persistent morbidity, hindering child development, diminishing productivity, and imposing economic burdens. Due to the emergence of drug resistance and limited management options, there is need to develop additional effective inhibitors for schistosomiasis. In view of this, quantitative structure-activity relationship studies, molecular docking, molecular dynamics simulations, drug-likeness and pharmacokinetics predictions were applied to 39 Schistosoma mansoni Thioredoxin Glutathione Reductase (SmTGR) inhibitors. The chosen QSAR model demonstrated robust statistical parameters, including an R2 of 0.798, R2adj of 0.767, Q2cv of 0.681, LOF of 0.930, R2test of 0.776, and cR2p of 0.746, confirming its reliability. The most active derivative (compound 40) was identified as a lead candidate for the development of new potential non-covalent inhibitors through ligand-based design. Subsequently, 12 novel compounds (40a-40l) were designed with enhanced anti-schistosomiasis activity and binding affinity. Molecular docking studies revealed strong and stable interactions, including hydrogen bonding, between the designed compounds and the target receptor. Molecular dynamics simulations over 100 nanoseconds and MM-PBSA free binding energy (ΔGbind) calculations validated the stability of the two best-designed molecules. Furthermore, drug-likeness and pharmacokinetics prediction analyses affirmed the potential of these designed compounds, suggesting their promise as innovative agents for the treatment of schistosomiasis.
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Affiliation(s)
- Saudatu Chinade Ja’afaru
- Department of Chemistry Ahmadu Bello University Zaria, Zaria, Nigeria
- Department of Chemistry, Aliko Dangote University of Science and Technology, Wudil, Kano, Nigeria
| | - Adamu Uzairu
- Department of Chemistry Ahmadu Bello University Zaria, Zaria, Nigeria
| | - Imren Bayil
- Department of Bioinformatics and Computational Biology, Gaziantep University, Gaziantep, Turkey
| | | | | | | | - Abu Tayab Moin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | | | - Nurul Absar
- Department of Biochemistry and Biotechnology, Faculty of Basic Medical and Pharmaceutical Sciences, University of Science & Technology Chittagong, Khulshi, Chittagong, Bangladesh
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Ja'afaru SC, Uzairu A, Chandra A, Sallau MS, Ndukwe GI, Ibrahim MT, Qamar I. Ligand based-design of potential schistosomiasis inhibitors through QSAR, homology modeling, molecular dynamics, pharmacokinetics, and DFT studies. J Taibah Univ Med Sci 2024; 19:429-446. [PMID: 38440085 PMCID: PMC10909894 DOI: 10.1016/j.jtumed.2024.02.003] [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: 11/08/2023] [Revised: 01/03/2024] [Accepted: 02/19/2024] [Indexed: 03/06/2024] Open
Abstract
Objectives Schistosomiasis, a neglected tropical disease, is a leading cause of mortality in affected geographic areas. Currently, because no vaccine for schistosomiasis is available, control measures rely on widespread administration of the drug praziquantel (PZQ). The mass administration of PZQ has prompted concerns regarding the emergence of drug resistance. Therefore, new therapeutic targets and potential compounds are necessary to combat schistosomiasis. Methods Twenty-four potent derivatives of PZQ were optimized via density functional theory (DFT) at the B3LYP/6-31G∗ level. Quantitative structureactivity relationship (QSAR) models were generated and statistically validated, and a lead candidate was selected to develop therapeutic options with improved efficacy against schistosomiasis. The biological and binding energies of the designed compounds were evaluated. In addition, molecular dynamics; drug-likeness; absorption, distribution, metabolism, excretion, and toxicity (ADMET); and DFT studies were performed on the newly designed compounds. Results Five QSAR models were generated, among which model 1 had favorable validation parameters (R2train: 0.957, R2adj: 0.941, LOF: 0.101, Q2cv: 0.906, and R2test: 0.783) and was chosen to identify a lead candidate. Other statistical parameters for the chosen model included variance inflation factor values ranging from 1.242 to 1.678, and a Y-scrambling coefficient (cRp2) of 0.747. Five new compounds were designed with improved predicted activity (ranging from 5.081 to 7.022) surpassing those of both the lead compound and PZQ (predicted pEC50 of 5.545). Molecular dynamics simulation revealed high binding affinity of the proposed compounds toward the target receptor. ADMET and drug-likeness assessments indicated adherence to Lipinski's rule of five criteria, thereby suggesting pharmacological and oral safety. In addition, DFT analysis indicated resistance to electronic alteration during chemical reactions. Conclusion The proposed compounds exhibited potential drug characteristics, thus indicating their suitability for further investigation to enhance schistosomiasis treatment options.
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Affiliation(s)
- Saudatu C. Ja'afaru
- Department of Chemistry, Ahmadu Bello University Zaria, Nigeria
- Department of Chemistry, Aliko Dangote University of Science and Technology, Wudil, Kano, Nigeria
| | - Adamu Uzairu
- Department of Chemistry, Ahmadu Bello University Zaria, Nigeria
| | - Anshuman Chandra
- School of Physical Sciences, JawaharLal Nehru University, New Delhi, India
| | | | | | | | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
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Poleboyina PK, Naik U, Pasha A, Ravinder D, Bhanothu S, Poleboyina SM, Amineni U, Pawar SC. Virtual Screening, Molecular Docking, and Dynamic Simulations Revealed TGF-β1 Potential Inhibitors to Curtail Cervical Cancer Progression. Appl Biochem Biotechnol 2024; 196:1316-1349. [PMID: 37392324 DOI: 10.1007/s12010-023-04608-5] [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] [Accepted: 06/19/2023] [Indexed: 07/03/2023]
Abstract
Cervical cancer is one of the main causes of cancer death in women globally, and its epidemiology is similar to that of a low-infectious venereal illness. Many sexual partners and early age at first intercourse have been demonstrated to have a significant influence on risk. TGF-β1 is a multifunctional cytokine that is required for cervical carcinoma metastasis, tumor development, progression, and invasion. The TGF-β1 signaling system plays a paradoxical function in cancer formation, suppressing early-stage tumor growth while increasing tumor progression and metastasis. Importantly, TGF-β1 and TGF-β receptor 1 (TGF-βR1), two components of the TGF-β signaling system, are substantially expressed in a range of cancers, including breast cancer, colon cancer, gastric cancer, and hepatocellular carcinoma. The current study aims to investigate possible inhibitors targeting TGF-β1 using molecular docking and dynamic simulations. To target TGF-β1, we used anti-cancer drugs and small molecules. MVD was utilized for virtual screening, and the highest scoring compound was then subjected to MD simulations using Schrodinger software package v2017-1 (Maestro v11.1) to identify the most favorable lead interactions against TGF-β1. The Nilotinib compound has shown the least XP Gscore of -2.581 kcal/mol, 30ns MD simulations revealing that the Nilotinib- TGF-β1 complex possesses the lowest energy of -77784.917 kcal/mol. Multiple parameters, including Root Mean Square Deviation, Root Mean Square Fluctuation, and Intermolecular Interactions, were used to analyze the simulation trajectory. Based on the results; we conclude that the ligand nilotinib appears to be a promising prospective TGF-β1inhibitor for reducing TGF-β1 expression ad halting cervical cancer progression.
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Affiliation(s)
- Pavan Kumar Poleboyina
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India
| | - Umakanth Naik
- Department of Bioinformatics, SVIMS University, Tirupati, Andhra Pradesh, 517 507, India
| | - Akbar Pasha
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India
| | - Doneti Ravinder
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India
| | - Shivaji Bhanothu
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India
| | - Sneha Malleswari Poleboyina
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India
| | - Umamaheshwari Amineni
- Department of Bioinformatics, SVIMS University, Tirupati, Andhra Pradesh, 517 507, India
| | - Smita C Pawar
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India.
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Poleboyina SM, Poleboyina PK, Pawar SC, Guntuku G. Homology Modeling, Screening, and Identification of Potential FOXO6 Inhibitors Curtail Gastric Cancer Progression: an In Silico Drug Repurposing Approach. Appl Biochem Biotechnol 2023; 195:7708-7737. [PMID: 37086375 DOI: 10.1007/s12010-023-04490-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 04/23/2023]
Abstract
Gastric cancer is the world's second leading cause of cancer-related fatalities, with the epidemiology changing over the previous several decades. FOXOs are the O subfamily of the forkhead box (FOX) transcription factor family, which consists of four members: FOXO1, FOXO3, FOXO4, and FOXO6. FOXO6 mRNA and protein levels are increased in gastric cancer tissues. FOXO6 forced overexpression enhances gastric cancer cell growth, while knockdown decreases proliferation. In our study, the GEPIA, Kaplan-Meier, KEGG, and STRING databases were used to determine FOXO6 mRNA expression, overall survival ratio, interactive pathways, and top 10 associated proteins in gastric cancer respectively. Due to the lack of a solved structure for FOXO6, homology modeling was performed to obtain a 3D structure model, and we used anti-cancer drugs and small molecules to target FOXO6 for identifying a potential selective FOXO6 inhibitor. The chemical composition of the proteins and ligands has a significant impact on docking procedure performance. With this in mind, a critical evaluation of the performance of three regularly used docking routines was carried out: MVD, AutoDock Vina in PyRx, and ArgusLab. The binding affinities, docking scores, and intermolecular interactions were used as assessment criteria. In the study, the porfimer sodium showed excellent binding affinity to the FOXO6 protein. The major three docking software packages were used to analyze the scoring/H-bonding energy and intermolecular interactions. Based on the results, we concluded that FOXO6 was upregulated in gastric cancer and the ligand porfimer sodium emerges as a promising potential FOXO6 inhibitor to curtail gastric cancer progression.
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Affiliation(s)
- Sneha Malleswari Poleboyina
- Department of Pharmaceutical Biotechnology, AU College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, Andhra Pradesh, 530003, India
| | - Pavan Kumar Poleboyina
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India
| | - Smita C Pawar
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India.
| | - Girijasankar Guntuku
- Department of Pharmaceutical Biotechnology, AU College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, Andhra Pradesh, 530003, India.
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Abdullahi SH, Uzairu A, Shallangwa GA, Uba S, Umar AB. Ligand-based drug design of quinazolin-4(3H)-ones as breast cancer inhibitors using QSAR modeling, molecular docking, and pharmacological profiling. J Egypt Natl Canc Inst 2023; 35:24. [PMID: 37544974 DOI: 10.1186/s43046-023-00182-3] [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: 04/04/2022] [Accepted: 07/12/2023] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND Breast cancer is the most common tumor among females globally. Its prevalence is growing around the world, and it is alleged to be the leading cause of cancer death. Approved anti-breast cancer drugs display several side effects and resistance during the early treatment stage. Hence, there is a need for the development of more effective and safer drugs. This research was aimed at designing more potent quinazolin-4(3H)-one molecules as breast cancer inhibitors using a ligand-based design approach, studying their modes of interaction with the target enzyme using molecular docking simulation, and predicting their pharmacological properties. METHODS The QSAR model was developed using a series of quinazoline-4(3H)-one derivatives by utilizing Material Studio v8.0 software and validated both internally and externally. Applicability domain virtual screening was utilized in selecting the template molecule, which was structurally modified to design more potent molecules. The inhibitive capacities of the design molecules were predicted using the developed model. Furthermore, molecular docking was performed with the EGFR target active site residues, which were obtained from the protein data bank online server (PDB ID: 2ITO) using Molegro Virtual Docker (MVD) software. SwissADME and pkCSM online sites were utilized in predicting the pharmacological properties of the designed molecules. RESULTS Four QSAR models were generated, and the first model was selected due to its excellent internal and external statistical parameters as follows: R2 = 0.919, R2adj = 0.898, Q2cv = 0.819, and R2pred = 0.7907. The robustness of the model was also confirmed by the result of the Y-scrambling test performed with cR2p = 0.7049. The selected model was employed to design seven molecules, with compound 4 (pIC50 = 5.18) adopted as the template. All the designed compounds exhibit better activities ranging from pIC50 = 5.43 to 5.91 compared to the template and Doruxybucin (pIC50 = 5.35). The results of molecular docking revealed better binding with the EGFR target compared with the template and Doruxybucin. The designed compounds exhibit encouraging therapeutic applicability, as evidenced by the findings of pharmacological property prediction. CONCLUSIONS The designed derivatives could be utilized as novel anti-breast cancer agents.
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Affiliation(s)
- Sagiru Hamza Abdullahi
- Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, Zaria, Kaduna State, P.M.B.1045, Nigeria.
| | - Adamu Uzairu
- Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, Zaria, Kaduna State, P.M.B.1045, Nigeria
| | - Gideon Adamu Shallangwa
- Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, Zaria, Kaduna State, P.M.B.1045, Nigeria
| | - Sani Uba
- Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, Zaria, Kaduna State, P.M.B.1045, Nigeria
| | - Abdullahi Bello Umar
- Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, Zaria, Kaduna State, P.M.B.1045, Nigeria
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Daoui O, Mali SN, Elkhattabi K, Elkhattabi S, Chtita S. Repositioning Cannabinoids and Terpenes as Novel EGFR-TKIs Candidates for Targeted Therapy Against Cancer: A virtual screening model using CADD and biophysical simulations. Heliyon 2023; 9:e15545. [PMID: 37128337 PMCID: PMC10148140 DOI: 10.1016/j.heliyon.2023.e15545] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/07/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023] Open
Abstract
This study examines the potential of Cannabis sativa L. plants to be repurposed as therapeutic agents for cancer treatment through designing of hybrid Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs). A set of 50 phytochemicals was taken from Cannabinoids and Terpenes and subjected for screening using Semi-flexible and Flexible Molecular Docking methods, MM-GBSA free binding energy computations, and pharmacokinetic/pharmacodynamic (ADME-Tox) predictions. Nine promising phytochemicals, Cannabidiolic acid (CBDA), Cannabidiol (CBD), Tetrahydrocannabivarin (THCV), Dronabinol (Δ-9-THC), Delta-8-Tetrahydrocannabinol (Δ-8-THC), Cannabicyclol (CBL), Delta9-tetrahydrocannabinolic acid (THCA), Beta-Caryophyllene (BCP), and Gamma-Elemene (γ-Ele) were identified as potential EGFR-TKIs natural product candidates for cancer therapy. To further validate these findings, a set of Molecular Dynamics simulations were conducted over a 200 ns trajectory. This hybrid early drug discovery screening strategy has the potential to yield a new generation of EGFR-TKIs based on natural cannabis products, suitable for cancer therapy. In addition, the application of this computational strategy in the virtual screening of both natural and synthetic chemical libraries could support the discovery of a wide range of lead drug agents to address numerous diseases.
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Affiliation(s)
- Ossama Daoui
- Laboratory of Engineering, Systems and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, P.O. Box 72, Fez, Morocco
- Corresponding author.
| | - Suraj N. Mali
- Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, India, 835215
| | - Kaouakeb Elkhattabi
- Department of Fundamental Sciences, Faculty of Dental Medicine, Mohammed V University in Rabat, Morocco
| | - Souad Elkhattabi
- Laboratory of Engineering, Systems and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, P.O. Box 72, Fez, Morocco
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, P.O. Box 7955, Casablanca, Morocco
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An insight into the rational design of recent purine-based scaffolds in targeting various cancer pathways. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Bakchi B, Krishna AD, Sreecharan E, Ganesh VBJ, Niharika M, Maharshi S, Puttagunta SB, Sigalapalli DK, Bhandare RR, Shaik AB. An overview on applications of SwissADME web tool in the design and development of anticancer, antitubercular and antimicrobial agents: A medicinal chemist's perspective. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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11
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Chemometric Study, Homology Modeling of G Protein-Coupled Bile Acids Receptor (GPBAR_HUMAN) of Type-2 Diabetes Mellitus, Virtual Screening Evaluation, Drug-Likeness and ADME Prediction for Newly Designed Compounds. Macromol Res 2022. [DOI: 10.1007/s13233-022-0071-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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12
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C S, S. DK, Ragunathan V, Tiwari P, A. S, P BD. Molecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease. J Biomol Struct Dyn 2022; 40:585-611. [PMID: 32897178 PMCID: PMC7573242 DOI: 10.1080/07391102.2020.1815584] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/21/2020] [Indexed: 12/31/2022]
Abstract
The study aims to evaluate the potency of two hundred natural antiviral phytocompounds against the active site of the Severe Acquired Respiratory Syndrome - Coronavirus - 2 (SARS-CoV-2) Main-Protease (Mpro) using AutoDock 4.2.6. The three- dimensional crystal structure of the Mpro (PDB Id: 6LU7) was retrieved from the Protein Data Bank (PDB), the active site was predicted using MetaPocket 2.0. Food and Drug Administration (FDA) approved viral protease inhibitors were used as standards for comparison of results. The compounds theaflavin-3-3'-digallate, rutin, hypericin, robustaflavone, and (-)-solenolide A with respective binding energy of -12.41 (Ki = 794.96 pM); -11.33 (Ki = 4.98 nM); -11.17 (Ki = 6.54 nM); -10.92 (Ki = 9.85 nM); and -10.82 kcal/mol (Ki = 11.88 nM) were ranked top as Coronavirus Disease - 2019 (COVID-19) Mpro inhibitors. The interacting amino acid residues were visualized using Discovery Studio 3.5 to elucidate the 2-dimensional and 3-dimensional interactions. The study was validated by i) re-docking the N3-peptide inhibitor-Mpro and superimposing them onto co-crystallized complex and ii) docking decoy ligands to Mpro. The ligands that showed low binding energy were further predicted for and pharmacokinetic properties and Lipinski's rule of 5 and the results are tabulated and discussed. Molecular dynamics simulations were performed for 50 ns for those compounds using the Desmond package, Schrödinger to assess the conformational stability and fluctuations of protein-ligand complexes during the simulation. Thus, the natural compounds could act as a lead for the COVID-19 regimen after in-vitro and in- vivo clinical trials.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shivanika C
- Department of Bio-Engineering, School of
Engineering, Vels Institute of Science Technology and Advanced Studies,
Chennai, Tamil Nadu, India
| | - Deepak Kumar S.
- Department of Biotechnology, Rajalakshmi
Engineering College, Thandalam, Tamil Nadu,
India
| | - Venkataraghavan Ragunathan
- Department of Chemical Engineering, Alagappa
College of Technology, Anna University, Chennai, Tamil
Nadu, India
| | - Pawan Tiwari
- Department of Pharmaceutical Science, Kumaun
University, Nainital, Uttarakhand,
India
| | - Sumitha A.
- Department of Pharmacology, ACS Medical
College and Hospital, Chennai, Tamil Nadu,
India
| | - Brindha Devi P
- Department of Bio-Engineering, School of
Engineering, Vels Institute of Science Technology and Advanced Studies,
Chennai, Tamil Nadu, India
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Adeniji SE, Arthur DE, Abdullahi M, Abdullahi A, Ugbe FA. Computer-aided modeling of triazole analogues, docking studies of the compounds on DNA gyrase enzyme and design of new hypothetical compounds with efficient activities. J Biomol Struct Dyn 2020; 40:4004-4020. [PMID: 33317403 DOI: 10.1080/07391102.2020.1852963] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The increasing problem of multi-drug resistant-tuberculosis has focused attention on developing new drugs that are not only active against drug-resistant tuberculosis, but also shorten the lengthy therapy. Therefore, this work employs the application of modeling technique to predict the inhibition activities of some prominent compounds which been reported to be efficient against Mycobacterium tuberculosis. To accomplish the purpose of this work, multiple regression and genetic function approximation were adopted to create the model. The established model was swayed with topological descriptors; MATS7s, SpMin4_Bhv, TDB3v and RDF70v. More also, interactions between the compounds and the target protein 'DNA gyrase' were evaluated via molecular docking approach utilizing the PyRx and discovery studio simulation software. Based on the docking analysis, compound 20 has the most noticeable binding affinity of -16.5 kcal/mol. Therefore, compound 20 served as a reference structural template and insight to design fourteen novel hypothetical agents with more prominent anti-tubercular activities. More also, compound 20j was observed with the highest activity among the designed compounds with a prominent binding affinity of -24.3 kcal/mol. Therefore, this research recommends in-vivo, in-vitro screening and pharmacokinetic properties to be carried out in order to determine the toxicity of the designed compounds.Communicated by Ramaswamy H. Sarma.
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Ibrahim MT, Uzairu A, Shallangwa GA, Uba S. Structure-based design of some quinazoline derivatives as epidermal growth factor receptor inhibitors. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020. [DOI: 10.1186/s43042-020-00107-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Abstract
Background
The discovery of epidermal growth factor receptor (EGFR) inhibitors for the treatment of lung cancer, most especially non-small cell lung cancer (NSCLC), was one of the major challenges encountered by the medicinal chemist in the world. The treatment of EGFR tyrosine kinase to manage NSCLCs becomes an urgent therapeutic necessity. NSCLC was the foremost cause of cancer mortality worldwide. Therefore, there is a need to develop more EGFR inhibitors due to the development of drug resistance by the mutation. This research is aimed at designing new EGFR inhibitors using a structure-based design approach. Structure-based drug design comprises several steps such as protein structure retrieval and preparation, ligand library preparation, docking, and structural modification on the best hit compound to design new ones.
Result
Molecular docking virtual screening on fifty sets of quinazoline derivatives/epidermal growth factor receptor inhibitors against their target protein (EGFR tyrosine kinase receptor PDB entry: 3IKA) and pharmacokinetic profile predictions were performed to identify hit compounds with promising affinities toward their target and good pharmacokinetic profiles. The hit compounds identified were compound 6 with a binding affinity of − 9.3 kcal/mol, compounds 5 and 8, each with a binding affinity of − 9.1 kcal/mol, respectively. The three hit compounds bound to EGFR tyrosine kinase receptor via four different types of interactions which include conventional hydrogen bond, carbon-hydrogen bond, electrostatic, and hydrophobic interactions, respectively. The best hit (compound 6) among the 3 hit compounds was retained as a template and used to design sixteen new EGFR inhibitors. The sixteen newly designed compounds were also docked into the active site of EGFR tyrosine kinase receptor to study their mode of interactions with the receptor. The binding affinities of these newly designed compounds range from − 9.5 kcal/mol to − 10.2 kcal/mol. The pharmacokinetic profile predictions of these newly designed compounds were further examined and found to be orally bioavailable with good absorption, low toxicity level, and permeable properties.
Conclusion
The sixteen newly designed EGFR inhibitors were found to have better binding affinities than the template used in the designing process and afatinib the positive control (an FDA approved EGFR inhibitor). None of these designed compounds was found to violate more than the permissible limit set by RO5. More so, the newly designed compounds were found to have good synthetic accessibility which indicates that these newly designed compounds can be easily synthesized in the laboratory.
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Lead Identification of Some Anti-Cancer Agents with Prominent Activity Against Non-small Cell Lung Cancer (NSCLC) and Structure-Based Design. CHEMISTRY AFRICA 2020. [DOI: 10.1007/s42250-020-00191-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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16
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Structure-based design and activity modeling of novel epidermal growth factor receptor kinase inhibitors; an in silico approach. SCIENTIFIC AFRICAN 2020. [DOI: 10.1016/j.sciaf.2020.e00503] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Ibrahim MT, Uzairu A, Uba S, Shallangwa GA. Computational virtual screening and structure-based design of some epidermal growth factor receptor inhibitors. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2020. [DOI: 10.1186/s43094-020-00074-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Abstract
Background
The foremost cause of cancer mortality worldwide was lung cancer. Lung cancer is divided into small cell lung cancer and non-small cell lung cancer (NSCLC). The latter is the main type of lung cancer that account for about 90% of the cancer issues and estimate about 25% of the cancer mortality each year in the world. Among the types of lung cancer with about 1.5 million patients and less than 20% survival rate is NSCLC. Overexpression of EGFR tyrosine kinase was recognized to be the cause of NSCLC. Therefore, there is a need to develop more EGFR inhibitors due to drug-resistance development by the mutation.
Result
Computational virtual screening on some epidermal growth factor receptor inhibitors (EGFRL858R/T790M inhibitors or NSCLC therapeutic agents) against their target protein (EGFR tyrosine kinase receptor pdb entry 3IKA) was performed via molecular docking simulation and pharmacokinetics to identify hit compounds with a promising affinity toward their target. The hit compounds discovered were compound 22 with −9.8 kcal/mol, 24 with −9.7 kcal/mol, 17 with −9.7 kcal/mol, and 19 with −9.5 kcal/mol respectively. These lead compounds were further subjected to drug-likeness and ADME prediction and found to be orally bioavailable. Six (6) new EGFRL858R/T790M inhibitors using compound 22 with the highest binding affinity as a template were designed.
Conclusion
The six newly EGFRL858R/T790M inhibitors were found to have a better binding affinity than the template used in the designing process and AZD9291 (the positive control). None of the designed compounds was found to violate more than the permissible limit set by RO5 thereby predicting their easy transportation, absorption, and diffusion. More so, the designed compounds were found to have good synthetic accessibility which indicates that these designed compounds can be easily synthesized in the laboratory.
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Adeniji SE, Adalumo OB. Computational modeling and ligand-based design of some novel hypothetical compound as prominent inhibitors against Mycobacterium tuberculosis. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2020. [DOI: 10.1186/s43094-020-00027-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Time consumed and expenses in discovering and synthesizing new hypothetical drugs with improved biological activity have been a major challenge toward the treatment of multi-drug-resistant strain Mycobacterium tuberculosis (TB). To solve the above problem, quantitative structure activity relationship (QSAR) is a recent approach developed to discover novel agents with better biological activity against M. tuberculosis.
Results
A validated QSAR model was developed in this study to predict the biological activities of some anti-tubercular compounds and to design new hypothetical drugs is influenced with the molecular descriptors, AATS7s, VR1_Dzi, VR1_Dzs, SpMin7_Bhe, and TDB8e, which has been validated through internal and external validation test. Prior to high anti-tubercular activity of the lead compound, compound 17 served as a template structure to design compounds with improved activity. Among the compounds designed, compounds 17i, 17j, and 17n were observed with improved anti-tubercular activities which ranges from 8.8981 to 9.0377 pBA.
Conclusion
The outcome of this research is recommended for pharmaceutical and medicinal chemists to synthesis and carry out an in vivo and in vitro screening for the proposed designed compounds in order to substantiate the computational findings.
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Adeniji SE, Arthur DE, Abdullahi M, Haruna A. Quantitative Structure–Activity Relationship Model, Molecular Docking Simulation and Computational Design of Some Novel Compounds Against DNA Gyrase Receptor. CHEMISTRY AFRICA-A JOURNAL OF THE TUNISIAN CHEMICAL SOCIETY 2020. [DOI: 10.1007/s42250-020-00132-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Adeniji SE, Adamu Shallangwa G, Ebuka Arthur D, Abdullahi M, Mahmoud AY, Haruna A. Quantum modelling and molecular docking evaluation of some selected quinoline derivatives as anti-tubercular agents. Heliyon 2020; 6:e03639. [PMID: 32258484 PMCID: PMC7114754 DOI: 10.1016/j.heliyon.2020.e03639] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 01/17/2020] [Accepted: 03/18/2020] [Indexed: 11/29/2022] Open
Abstract
Mycobacterium tuberculosis has instigated a serious challenge toward the effective treatment of tuberculosis. The reoccurrence of the resistant strains of the disease to accessible drugs/medications has mandate for the development of more effective anti-tubercular agents with efficient activities. Time expended and costs in discovering and synthesizing new hypothetical drugs with improved biological activity have been a major challenge toward the treatment of multi-drug resistance strain M. tuberculosis (TB). Meanwhile, to solve the problem stated, a new approach i.e. QSAR which establish connection between novel drugs with a better biological against M. tuberculosis is adopted. The anti-tubercular model established in this study to forecast the biological activities of some anti-tubercular compounds selected and to design new hypothetical drugs is subjective to the molecular descriptors; AATS7s, VE2_Dzi, SpMin7-Bhe and RDF110i. The significant of the model were observed with R2 of 0.8738, R2 adj of 0.8351 Q_cvˆ2 of 0.7127 which served as criteria to substantiate the QSAR model. More also, the model significant with the QSAR external validation criterial ‘‘(R2test) of 0.7532. Ligand-receptor interactions between quinoline derivatives and the receptor (DNA gyrase) was carried out using molecular docking technique by employing the PyRx virtual screening software and discovery studio visualizer software. Furthermore, docking study indicates that compounds 10 of the derivatives with promising biological activity have the utmost binding energy of -18.8 kcal/mol. Meanwhile, the interaction of the standard drug; isoniazid with the target enzyme was observed with the binding energy -14.6 kcal/mol which was significantly lesser than the binding energy of the ligand (compound 10). This implies that ligand 10 could be used as a structural template to design better hypothetical anti-tubercular drugs with more efficient activities. The presumption of this research aid the medicinal chemists and pharmacist to design and synthesis a novel drug candidate against the tuberculosis. Moreover, in-vitro and in-vivo test could be carried out to validate the computational results.
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Affiliation(s)
| | | | | | | | - A Y Mahmoud
- Chemistry Department, Ahmadu Bello University, Zaria Nigeria
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