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Wani MA, Banerjee A, Garg P. Computer-aided drug design approaches for the identification of potent inhibitors targeting elongation factor G of Mycobacterium tuberculosis. J Mol Graph Model 2025; 136:108954. [PMID: 39854882 DOI: 10.1016/j.jmgm.2025.108954] [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] [Received: 12/17/2024] [Revised: 01/08/2025] [Accepted: 01/15/2025] [Indexed: 01/27/2025]
Abstract
Elongation factor G (EF-G) is essential for protein synthesis in Mycobacterium tuberculosis (Mtb), positioning it as a promising target for anti-tubercular drug development. This study employs Structure-Based Drug Design (SBDD) to identify potential small molecule inhibitors that specifically target EF-G. Initially, binding hotspots on EF-G were pinpointed, and the binding modes of various compounds were analyzed. Through protein-protein interaction studies, several promising candidates were validated. Virtual screening and molecular docking techniques were utilized to evaluate the binding affinities and interactions of 20 candidate molecules with Mtb EF-G. Additionally, toxicity profiles of these compounds were assessed using predictive models, which indicated non-carcinogenic properties. To further refine the selection process, Support Vector Machine (SVM) and Random Forest models were applied to predict cell wall permeability. Notably, Asinex (8853) and Asinex (102619) emerged as top candidates, boasting high probability scores for effective permeability. Molecular docking and molecular dynamics (MD) simulations revealed that Asinex (8853), Asinex (102619), and Otava (79226) exhibited strong binding affinities and favorable conformations within the active site of Mtb EF-G. These findings suggest that these compounds have significant potential as inhibitors, warranting further investigation into their efficacy as novel anti-tubercular agents. Overall, this study emphasizes the value of Structure-Based Drug Design in identifying promising therapeutic candidates against tuberculosis by targeting essential bacterial factors like EF-G.
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Affiliation(s)
- Mushtaq Ahmad Wani
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, 160062, Punjab, India
| | - Aritra Banerjee
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, 160062, Punjab, India
| | - Prabha Garg
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, 160062, Punjab, India.
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2
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Mostafa RM, Baz MM, Ebeed HT, Essawy HS, Dawwam GE, Darwish AB, Selim A, El-Shourbagy NM. Biological effects of Bougainvillea glabra, Delonix regia, Lantana camara, and Platycladus orientalis extracts and their possible metabolomics therapeutics against the West Nile virus vector, Culex pipiens (Diptera: Culicidae). Microb Pathog 2024; 195:106870. [PMID: 39163920 DOI: 10.1016/j.micpath.2024.106870] [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] [Received: 06/05/2024] [Revised: 08/15/2024] [Accepted: 08/17/2024] [Indexed: 08/22/2024]
Abstract
Plants are a treasure trove of biological materials containing a wide range of potential phytochemicals that are target-specific, rapidly biodegradable, and environmentally friendly, with multiple medicinal effects. Unfortunately, the development of resistance to synthetic pesticides and antibiotics led to the discovery of new antibiotics, antioxidants, and biopesticides. This has also led to the creation of new medications that work very well. The current study aimed to prove that ornamental plants contain specialized active substances that are used in several biological processes. Mosquitoes, one of the deadliest animals on the planet, cause millions of fatalities each year by transmitting several human illnesses. Phytochemicals are possible biological agents for controlling pests that are harmful. The potential of leaf extracts of Bougainvillea glabra, Delonix regia, Lantana camara, and Platycladus orientalis against Culex pipiens and microbial agents was evaluated. Acetone extracts had more toxic effects against Cx. pipiens larvae (99.0-100 %, 72 h post-treatment), and the LC50 values were 142.8, 189.5, 95.4, and 71.1 ppm for B. glabra, D. regia, L. camara, and P. orientalis, respectively. Plant extracts tested in this study showed high insecticidal, antimicrobial, and antioxidant potential. GC-MS and HPLC analyses showed a higher number of terpenes, flavonoids, and phenolic compounds. The ADME analysis of element, caryophyllene oxide, caryophyllene, and copaene showed that they were similar to drugs and that they were better absorbed by the body and able to pass through the blood-brain barrier. Our results confirm the ability of ornamental plants to have promising larvicidal and antimicrobial activity and biotechnology.
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Affiliation(s)
- Reham M Mostafa
- Botany and Microbiology Department, Faculty of Science, Benha University, Benha, Qalyubiya, 13518, Egypt
| | - Mohamed M Baz
- Entomology Department, Faculty of Science, Benha University, Benha, 13518, Egypt.
| | - Heba Talat Ebeed
- Botany and Microbiology Department, Faculty of Science, Damietta University, Damietta, 34517, Egypt; National Biotechnology Network of Expertise (NBNE), Academy of Scientific Research and Technology (ASRT), Cairo, Egypt
| | - Heba S Essawy
- Botany and Microbiology Department, Faculty of Science, Benha University, Benha, Qalyubiya, 13518, Egypt
| | - Ghada E Dawwam
- Botany and Microbiology Department, Faculty of Science, Benha University, Benha, Qalyubiya, 13518, Egypt
| | - Ahmed B Darwish
- Zoology Department, Faculty of Science, Suez University, Suez, 43518, Egypt
| | - Abdelfattah Selim
- Department of Animal Medicine (Infectious Diseases), College of Veterinary Medicine, Benha University Toukh, 13736, Egypt.
| | - Nancy M El-Shourbagy
- Entomology Department, Faculty of Science, Benha University, Benha, 13518, Egypt
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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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5
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Abdullahi M, Uzairu A, Shallangwa GA, Mamza PA, Ibrahim MT, Chandra A, Goel VK. In-silico molecular modelling studies of some camphor imine based compounds as anti-influenza A (H1N1) pdm09 virus agents. J Biomol Struct Dyn 2024; 42:2013-2033. [PMID: 37166274 DOI: 10.1080/07391102.2023.2209654] [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] [Received: 01/04/2023] [Accepted: 04/09/2023] [Indexed: 05/12/2023]
Abstract
The advent of influenza A (H1N1) drug-resistant strains led to the search quest for more potent inhibitors of the influenza A virus, especially in this devastating COVID-19 pandemic era. Hence, the present research utilized some molecular modelling strategies to unveil new camphor imine-based compounds as anti-influenza A (H1N1) pdm09 agents. The 2D-QSAR results revealed GFA-MLR (R2train = 0.9158, Q2=0.8475) and GFA-ANN (R2train = 0.9264, Q2=0.9238) models for the anti-influenza A (H1N1) pdm09 activity prediction which have passed the QSAR model acceptability thresholds. The results from the 3D-QSAR studies also revealed CoMFA (R2train =0.977, Q2=0.509) and CoMSIA_S (R2train =0.976, Q2=0.527) models for activity predictions. Based on the notable information derived from the 2D-QSAR, 3D-QSAR, and docking analysis, ten (10) new camphor imine-based compounds (22a-22j) were designed using the most active compound 22 as the template. Furthermore, the high predicted activity and binding scores of compound 22j were further justified by the high reactive sites shown in the electrostatic potential maps and other quantum chemical calculations. The MD simulation of 22j in the active site of the influenza hemagglutinin (HA) receptor confirmed the dynamic stability of the complex. Moreover, the appraisals of drug-likeness and ADMET properties of the proposed compounds showed zero violation of Lipinski's criteria with good pharmacokinetic profiles. Hence, the outcomes in this work recommend further in-depth in vivo and in-vitro investigations to validate these theoretical findings.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mustapha Abdullahi
- Faculty of Physical Sciences, Department of Chemistry, Ahmadu Bello University, Zaria, Kaduna State, Nigeria
- Faculty of Sciences, Department of Pure and Applied Chemistry, Kaduna State University, Zaria, Kaduna State, Nigeria
| | - Adamu Uzairu
- Faculty of Physical Sciences, Department of Chemistry, Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | - Gideon Adamu Shallangwa
- Faculty of Physical Sciences, Department of Chemistry, Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | - Paul Andrew Mamza
- Faculty of Physical Sciences, Department of Chemistry, Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | - Muhammad Tukur Ibrahim
- Faculty of Physical Sciences, Department of Chemistry, Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | - Anshuman Chandra
- School of Physical Science, Jawaharlal Nehru University, New Delhi, Delhi, India
| | - Vijay Kumar Goel
- School of Physical Science, Jawaharlal Nehru University, New Delhi, Delhi, India
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6
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Dougnon G, Ito M. Molecular Descriptors and QSAR Models for Sedative Activity of Sesquiterpenes Administered to Mice via Inhalation. PLANTA MEDICA 2023; 89:1236-1249. [PMID: 35158383 DOI: 10.1055/a-1770-7581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Essential oils are often utilized for therapeutic purposes and are composed of complex structural molecules, including sesquiterpenes, with high molecular weight and potential for stereochemistry. A detailed study on the properties of selected sesquiterpenes was conducted as part of a broader investigation on the effects of sesquiterpenes on the central nervous system. A set of 18 sesquiterpenes, rigorously selected from an original list of 114, was divided into 2 groups i.e., the training and test sets, with each containing 9 compounds. The training set was evaluated for the sedative activity in mice through inhalation, and all compounds were sedatives at any dose in the range of 4 × 10-4-4 × 10-2 mg/cage, except for curzerene. Molecular determinants of the sedative activities of sesquiterpenes were evaluated using quantitative structure-activity relationship (QSAR) and structure-activity relationship (SAR) analyses. An additional test set of six compounds obtained from the literature was utilized for validating the QSAR model. The parental carbonyl cation and an oxygen-containing groups are possible determinants of sedative activity. The QSAR study using multiple regression models could reasonably predict the sedative activity of sesquiterpenes with statistical parameters such as the correlation coefficient r2 = 0.82 > 0.6 and q2 LOO = 0.71 > 0.5 obtained using the leave-one-out cross-validation technique. Molar refractivity and the number of hydrogen bond acceptors were statistically important in predicting the activities. The present study could help predict the sedative activity of additional sesquiterpenes, thus accelerating the process of drug development.
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Affiliation(s)
- Godfried Dougnon
- Department of Pharmacognosy, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Michiho Ito
- Department of Pharmacognosy, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
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7
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Chowdhury H, Kumar Bera A, Subhasmita Raut S, Chandra Malick R, Sekhar Swain H, Saha A, Kumar Das B. In Vitro Antibacterial Efficacy of Cymbopogon flexuosus Essential Oil against Aeromonas hydrophila of Fish Origin and in Silico Molecular Docking of the Essential Oil Components against DNA Gyrase-B and Their Drug-Likeness. Chem Biodivers 2023; 20:e202200668. [PMID: 36799768 DOI: 10.1002/cbdv.202200668] [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: 07/21/2022] [Revised: 01/31/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023]
Abstract
In aquaculture, diseases caused by the Aeromonads with high antibiotic resistance are among the most common and troublesome diseases. Application of herbs is emerging as a tool in controlling these diseases. Plant extracts besides disease control, favor various physiological activities in fish. In this study, essential oil of Cymbopogon flexuosus (Poaceae family) was studied in vitro for its antibacterial efficacy against two oxytetracycline (OTC) resistant and one sensitive strains of Aeromonas hydrophila. The oil was found rich (86.93 %) in oxygenated terpenoids containing 74.15 % of citral. The oil exhibited dose dependent growth inhibition of the bacteria. Mean MIC value of the oil against the sensitive strain was recorded as 2.0 mg mL-1 whereas MBC value was recorded as 4.0 mg mL-1 . The oil was found effective against the OTC resistant isolates with the MIC and MBC values ranging from 2.67-3.33 and 4.0-6.67 mg mL-1 , respectively. In silico molecular docking of the essential oil components against DNA gyrase-B, a vital macromolecule in bacterial cell, was carried out to computationally asses the efficacy of the oil against the bacteria. Some of the components of the essential oil strongly bonded with the enzyme to inhibit its efficacy. Binding energy of some components of the oil was comparable to that of the conventional antibiotic, OTC. The identified phytochemicals exhibited favorable physicochemical and pharmacokinetic properties and satisfied the rule of five (Ro5).
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Affiliation(s)
- Hemanta Chowdhury
- ICAR - Central Inland Fisheries Research Institute, Manirampore, Barrackpore, Kolkata 700 120, West Bengal, India
| | - Asit Kumar Bera
- ICAR - Central Inland Fisheries Research Institute, Manirampore, Barrackpore, Kolkata 700 120, West Bengal, India
| | - Subhashree Subhasmita Raut
- ICAR - Central Inland Fisheries Research Institute, Manirampore, Barrackpore, Kolkata 700 120, West Bengal, India
| | - Ramesh Chandra Malick
- ICAR - Central Inland Fisheries Research Institute, Manirampore, Barrackpore, Kolkata 700 120, West Bengal, India
| | - Himanshu Sekhar Swain
- ICAR - Central Inland Fisheries Research Institute, Manirampore, Barrackpore, Kolkata 700 120, West Bengal, India
| | - Ajoy Saha
- ICAR - Central Inland Fisheries Research Institute, Manirampore, Barrackpore, Kolkata 700 120, West Bengal, India
| | - Basanta Kumar Das
- ICAR - Central Inland Fisheries Research Institute, Manirampore, Barrackpore, Kolkata 700 120, West Bengal, India
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8
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El fadili M, Er-rajy M, Imtara H, Noman OM, Mothana RA, Abdullah S, Zerougui S, Elhallaoui M. QSAR, ADME-Tox, molecular docking and molecular dynamics simulations of novel selective glycine transporter type 1 inhibitors with memory enhancing properties. Heliyon 2023; 9:e13706. [PMID: 36865465 PMCID: PMC9971180 DOI: 10.1016/j.heliyon.2023.e13706] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
A structural class of forty glycine transporter type 1 (GlyT1) inhibitors, was examined using molecular modeling techniques. The quantitative structure-activity relationships (QSAR) technology confirmed that human GlyT1 activity is strongly and significantly affected by constitutional, geometrical, physicochemical and topological descriptors. ADME-Tox in-silico pharmacokinetics revealed that L28 and L30 ligands were predicted as non-toxic inhibitors with a good ADME profile and the highest probability to penetrate the central nervous system (CNS). Molecular docking results indicated that the predicted inhibitors block GlyT1, reacting specifically with Phe319, Phe325, Tyr123, Tyr 124, Arg52, Asp475, Ala117, Ala479, Ile116 and Ile483 amino acids of the dopamine transporter (DAT) membrane protein. These results were qualified and strengthened using molecular dynamics (MD) study, which affirmed that the established intermolecular interactions for (L28, L30-DAT protein) complexes remain perfectly stable along 50 ns of MD simulation time. Therefore, they could be strongly recommended as therapeutics in medicine to improve memory performance.
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Affiliation(s)
- Mohamed El fadili
- LIMAS Laboratory, Faculty of Sciences Dhar El Mehraz, Sidi Mohammed Ben Abdellah University, BP 1796 Atlas, Fez 30000, Morocco
| | - Mohammed Er-rajy
- LIMAS Laboratory, Faculty of Sciences Dhar El Mehraz, Sidi Mohammed Ben Abdellah University, BP 1796 Atlas, Fez 30000, Morocco
| | - Hamada Imtara
- Faculty of Arts and Sciences, Arab American University Palestine, Jenin BP Box 240, Palestine
| | - Omar M. Noman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ramzi A. Mothana
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Sheaf Abdullah
- Department of Hand Surgery and Microsurgery, University Medicine Greifswald, Greifswald, Germany
| | - Sara Zerougui
- LIMAS Laboratory, Faculty of Sciences Dhar El Mehraz, Sidi Mohammed Ben Abdellah University, BP 1796 Atlas, Fez 30000, Morocco
| | - Menana Elhallaoui
- LIMAS Laboratory, Faculty of Sciences Dhar El Mehraz, Sidi Mohammed Ben Abdellah University, BP 1796 Atlas, Fez 30000, Morocco
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Ameen F, Orfali R, Mamidala E, Davella R. In silico toxicity prediction, molecular docking studies and in vitro validation of antibacterial potential of alkaloids from Eclipta alba in designing of novel antimicrobial therapeutic strategies. Biotechnol Genet Eng Rev 2022:1-15. [PMID: 36578142 DOI: 10.1080/02648725.2022.2162264] [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: 11/30/2022] [Accepted: 12/20/2022] [Indexed: 12/30/2022]
Abstract
The rapid emergence of various drug resistance and unfavourable aliphatic medication side effects endangers people's health. Phytocompounds with antibacterial activity and less harmful effects are known to be present in medicinal plants. Alkaloids from Eclipta alba were tested for their in vitro antibacterial capabilities and in silico docking studies against pathogenic bacteria and their target proteins in the current investigation. The alkaloid compounds verazine, ecliptine, 4-hydroxyverazine, 20-Epi-4beta-hydroxyverazine and hydroxyverazine were subjected to molecular docking studies to determine the method of binding as well as potential interactions and the docking score. The in vitro antibacterial activity of verazine alkaloid was assessed against two gram-positive and two gram-negative bacteria. Verazine alkaloid has the best inhibitory ability against DNA gyrase of E. coli (ΔG= -8.44 kcal/mol) and dihydrofolate reductase (DHFR) of S. aureus (ΔG= -10.04 kcal/mol), according to docking studies. Verazine shown substantial in vitro antibacterial activity in this investigation against all test bacteria, with MIC and MBC values of 31.25 and 62.50 µg/mL for S. aureus and 15.63 and 31.25 µg/mL for B. cereus, respectively. The results of this work highlighted the value of unique alkaloid compounds from E. alba, which may offer effective antibacterial agents and DNA gyrase, DHFR inhibitors due to their novel structural properties capable of combating antimicrobial resistance. These findings call for more investigation into the compounds' function as antibacterial agents, as well as their unique-binding locations and mechanisms.
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Affiliation(s)
- Fuad Ameen
- Department of Botany & Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Raha Orfali
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Estari Mamidala
- Department of Zoology, Infectious Diseases Research Lab, Kakatiya University, Warangal, India
| | - Rakesh Davella
- Department of Zoology, Infectious Diseases Research Lab, Kakatiya University, Warangal, India
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Ambiar MF, Aditsania A, Kurniawan I. QSAR Study on Falcipain Inhibitors as Anti-malaria using Genetic Algorithm-Support Vector Machine. 2022 5TH INTERNATIONAL CONFERENCE OF COMPUTER AND INFORMATICS ENGINEERING (IC2IE) 2022:287-293. [DOI: 10.1109/ic2ie56416.2022.9970052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
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Abdullahi M, Uzairu A, Shallangwa GA, Mamza PA, Ibrahim MT. Computational modelling studies of some 1,3-thiazine derivatives as anti-influenza inhibitors targeting H1N1 neuraminidase via 2D-QSAR, 3D-QSAR, molecular docking, and ADMET predictions. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2022; 11:104. [PMID: 36000144 PMCID: PMC9389500 DOI: 10.1186/s43088-022-00280-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/27/2022] [Indexed: 12/19/2022] Open
Abstract
Abstract
Background
Influenza virus disease remains one of the most contagious diseases that aided the deaths of many patients, especially in this COVID-19 pandemic era. Recent discoveries have shown that the high prevalence of influenza and SARS-CoV-2 coinfection can rapidly increase the death rate of patients. Hence, it became necessary to search for more potent inhibitors for influenza disease therapy. The present study utilized some computational modeling concepts such as 2D-QSAR, 3D-QSAR, molecular docking simulation, and ADMET predictions of some 1,3-thiazine derivatives as inhibitors of influenza neuraminidase (NA).
Results
The 2D-QSAR modeling results showed GFA-MLR ($$R_{{\text{train }}}^{2}$$
R
train
2
= 0.9192, Q2 = 0.8767, R2adj = 0.8991, RMSE = 0.0959, $$R_{{{\text{test}}}}^{2}$$
R
test
2
= 0.8943, $$R_{{{\text{pred}}}}^{2}$$
R
pred
2
= 0.7745) and GFA-ANN ($$R_{{\text{train }}}^{2}$$
R
train
2
= 0.9227, Q2 = 0.9212, RMSE = 0.0940, $$R_{{{\text{test}}}}^{2}$$
R
test
2
= 0.8831, $$R_{{{\text{pred}}}}^{2}$$
R
pred
2
= 0.7763) models with the computed descriptors as ATS7s, SpMax5_Bhv, nHBint6, and TDB9m for predicting the NA inhibitory activities of compounds which have passed the global criteria of accepting QSAR model. The 3D-QSAR modeling was carried out based on the comparative molecular field analysis (CoMFA) and comparative similarity indices analysis (CoMSIA). The CoMFA_ES ($$R_{{\text{train }}}^{2}$$
R
train
2
= 0.9620, Q2 = 0.643) and CoMSIA_SED ($$R_{{\text{train }}}^{2}$$
R
train
2
= 0.8770, Q2 = 0.702) models were found to also have good and reliable predicting ability. The compounds were also virtually screened based on their binding scores via molecular docking simulations with the active site of the NA (H1N1) target receptor which also confirms their resilient potency. Four potential lead compounds (4, 7, 14, and 15) with the relatively high inhibitory rate (> 50%) and docking (> − 6.3 kcal/mol) scores were identified as the possible lead candidates for in silico exploration of improved anti-influenza agents.
Conclusion
The drug-likeness and ADMET predictions of the lead compounds revealed non-violation of Lipinski’s rule and good pharmacokinetic profiles as important guidelines for rational drug design. Hence, the outcome of this research set a course for the in silico design and exploration of novel NA inhibitors with improved potency.
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3D-QSAR, ADME-Tox In Silico Prediction and Molecular Docking Studies for Modeling the Analgesic Activity against Neuropathic Pain of Novel NR2B-Selective NMDA Receptor Antagonists. Processes (Basel) 2022. [DOI: 10.3390/pr10081462] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A new class of selective antagonists of the N-Methyl-D-Aspartate (NMDA) receptor subunit 2B have been developed using molecular modeling techniques. The three-dimensional quantitative structure–activity relationship (3D-QSAR) study, based on comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) models, indicate that steric, electrostatic and hydrogen bond acceptor fields have a key function in the analgesic activity against neuropathic pain. The predictive accuracy of the developed CoMFA model (Q2 = 0.540, R2 = 0.980, R2 pred = 0.613) and the best CoMSIA model (Q2 = 0.665, R2 = 0.916, R2 pred = 0.701) has been successfully examined through external and internal validation. Based on ADMET in silico properties, L1, L2 and L3 ligands are non-toxic inhibitors of 1A2, 2C19 and 2C9 cytochromes, predicted to passively cross the blood–brain barrier (BBB) and have the highest probability to penetrate the central nervous system (CNS). Molecular docking results indicate that the active ligands (L1, L2 and L3) interact specifically with Phe176, Glu235, Glu236, Gln110, Asp136 and Glu178 amino acids of the transport protein encoded as 3QEL. Therefore, they could be used as analgesic drugs for the treatment of neuropathic pain.
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Khamouli S, Belaidi S, Bakhouch M, Chtita S, Hashmi MA, Qais FA. QSAR modeling, molecular docking, ADMET prediction and molecular dynamics simulations of some 6-arylquinazolin-4-amine derivatives as DYRK1A inhibitors. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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El fadili M, Er-Rajy M, Kara M, Assouguem A, Belhassan A, Alotaibi A, Mrabti NN, Fidan H, Ullah R, Ercisli S, Zarougui S, Elhallaoui M. QSAR, ADMET In Silico Pharmacokinetics, Molecular Docking and Molecular Dynamics Studies of Novel Bicyclo (Aryl Methyl) Benzamides as Potent GlyT1 Inhibitors for the Treatment of Schizophrenia. Pharmaceuticals (Basel) 2022; 15:670. [PMID: 35745588 PMCID: PMC9228289 DOI: 10.3390/ph15060670] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 02/04/2023] Open
Abstract
Forty-four bicyclo ((aryl) methyl) benzamides, acting as glycine transporter type 1 (GlyT1) inhibitors, are developed using molecular modeling techniques. QSAR models generated by multiple linear and non-linear regressions affirm that the biological inhibitory activity against the schizophrenia disease is strongly and significantly correlated with physicochemical, geometrical and topological descriptors, in particular: Hydrogen bond donor, polarizability, surface tension, stretch and torsion energies and topological diameter. According to in silico ADMET properties, the most active ligands (L6, L9, L30, L31 and L37) are the molecules having the highest probability of penetrating the central nervous system (CNS), but the molecule 32 has the highest probability of being absorbed by the gastrointestinal tract. Molecular docking results indicate that Tyr124, Phe43, Phe325, Asp46, Phe319 and Val120 amino acids are the active sites of the dopamine transporter (DAT) membrane protein, in which the most active ligands can inhibit the glycine transporter type 1 (GlyT1). The results of molecular dynamics (MD) simulation revealed that all five inhibitors remained stable in the active sites of the DAT protein during 100 ns, demonstrating their promising role as candidate drugs for the treatment of schizophrenia.
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Affiliation(s)
- Mohamed El fadili
- Engineering Materials, Modeling and Environmental Laboratory, Faculty of Sciences Dhar El Mehraz, Sidi Mohammed Ben Abdellah University, Fez 30000, Morocco; (M.E.-R.); (N.N.M.); (S.Z.); (M.E.)
| | - Mohammed Er-Rajy
- Engineering Materials, Modeling and Environmental Laboratory, Faculty of Sciences Dhar El Mehraz, Sidi Mohammed Ben Abdellah University, Fez 30000, Morocco; (M.E.-R.); (N.N.M.); (S.Z.); (M.E.)
| | - Mohammed Kara
- Laboratory of Biotechnology, Conservation and Valorisation of Naturals Resources, Faculty of Sciences Dhar El Mehraz, Sidi Mohamed Ben Abdellah University, Fez 30000, Morocco
| | - Amine Assouguem
- Laboratory of Functional Ecology and Environment, Faculty of Sciences and Technology, Sidi Mohamed Ben Abdellah University, Imouzzer Street, Fez 30000, Morocco;
| | - Assia Belhassan
- Molecular Chemistry and Natural Substances Laboratory, Department of Chemistry, Faculty of Sciences, University Moulay Ismail, Meknes 50000, Morocco;
| | - Amal Alotaibi
- Department of Basic Science, College of Medicine, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia;
| | - Nidal Naceiri Mrabti
- Engineering Materials, Modeling and Environmental Laboratory, Faculty of Sciences Dhar El Mehraz, Sidi Mohammed Ben Abdellah University, Fez 30000, Morocco; (M.E.-R.); (N.N.M.); (S.Z.); (M.E.)
| | - Hafize Fidan
- Department of Tourism and Culinary Management, Faculty of Economics, University of Food Technologies, 4000 Plovdiv, Bulgaria;
| | - Riaz Ullah
- Department of Pharmacognosy (MAPPRC), College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Sezai Ercisli
- Department of Horticulture, Agricultural Faculty, Ataturk University, Erzurum TR-25240, Turkey;
| | - Sara Zarougui
- Engineering Materials, Modeling and Environmental Laboratory, Faculty of Sciences Dhar El Mehraz, Sidi Mohammed Ben Abdellah University, Fez 30000, Morocco; (M.E.-R.); (N.N.M.); (S.Z.); (M.E.)
| | - Menana Elhallaoui
- Engineering Materials, Modeling and Environmental Laboratory, Faculty of Sciences Dhar El Mehraz, Sidi Mohammed Ben Abdellah University, Fez 30000, Morocco; (M.E.-R.); (N.N.M.); (S.Z.); (M.E.)
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Abishad P, Niveditha P, Unni V, Vergis J, Kurkure NV, Chaudhari S, Rawool DB, Barbuddhe SB. In silico molecular docking and in vitro antimicrobial efficacy of phytochemicals against multi-drug-resistant enteroaggregative Escherichia coli and non-typhoidal Salmonella spp. Gut Pathog 2021; 13:46. [PMID: 34273998 PMCID: PMC8286599 DOI: 10.1186/s13099-021-00443-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/08/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND In the wake of emergence of antimicrobial resistance, bioactive phytochemical compounds are proving to be important therapeutic agents. The present study envisaged in silico molecular docking as well as in vitro antimicrobial efficacy screening of identified phytochemical ligands to the dispersin (aap) and outer membrane osmoporin (OmpC) domains of enteroaggregative Escherichia coli (EAEC) and non-typhoidal Salmonella spp. (NTS), respectively. MATERIALS AND METHODS The evaluation of drug-likeness, molecular properties, and bioactivity of the identified phytocompounds (thymol, carvacrol, and cinnamaldehyde) was carried out using Swiss ADME, while Protox-II and StopTox servers were used to identify its toxicity. The in silico molecular docking of the phytochemical ligands with the protein motifs of dispersin (PDB ID: 2jvu) and outer membrane osmoporin (PDB ID: 3uu2) were carried out using AutoDock v.4.20. Further, the antimicrobial efficacy of these compounds against multi-drug resistant EAEC and NTS strains was determined by estimating the minimum inhibitory concentrations and minimum bactericidal concentrations. Subsequently, these phytochemicals were subjected to their safety (sheep and human erythrocytic haemolysis) as well as stability (cationic salts, and pH) assays. RESULTS All the three identified phytochemicals ligands were found to be zero violators of Lipinski's rule of five and exhibited drug-likeness. The compounds tested were categorized as toxicity class-4 by Protox-II and were found to be non- cardiotoxic by StopTox. The docking studies employing 3D model of dispersin and ompC motifs with the identified phytochemical ligands exhibited good binding affinity. The identified phytochemical compounds were observed to be comparatively stable at different conditions (cationic salts, and pH); however, a concentration-dependent increase in the haemolytic assay was observed against sheep as well as human erythrocytes. CONCLUSIONS In silico molecular docking studies provided useful insights to understand the interaction of phytochemical ligands with protein motifs of pathogen and should be used routinely before the wet screening of any phytochemicals for their antibacterial, stability, and safety aspects.
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Affiliation(s)
- Padikkamannil Abishad
- Department of Veterinary Public Health, College of Veterinary and Animal Sciences, KVASU, 673 576, Pookode, Wayanad, India
| | - Pollumahanti Niveditha
- ICAR-National Research Centre on Meat, Chengicherla, Boduppal Post, 500 092, Hyderabad, India
| | - Varsha Unni
- Department of Veterinary Public Health, College of Veterinary and Animal Sciences, KVASU, 673 576, Pookode, Wayanad, India
| | - Jess Vergis
- Department of Veterinary Public Health, College of Veterinary and Animal Sciences, KVASU, 673 576, Pookode, Wayanad, India
| | | | - Sandeep Chaudhari
- Nagpur Veterinary College, MAFSU, Seminary Hills, 440 006, Nagpur, India
| | - Deepak Bhiwa Rawool
- ICAR-National Research Centre on Meat, Chengicherla, Boduppal Post, 500 092, Hyderabad, India
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Arwansyah A, Arif AR, Syahputra G, Sukarti S, Kurniawan I. Theoretical studies of Thiazolyl-Pyrazoline derivatives as promising drugs against malaria by QSAR modelling combined with molecular docking and molecular dynamics simulation. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1935926] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Arwansyah Arwansyah
- Department of Chemistry, Faculty of Science, Universitas Cokroaminoto Palopo, Palopo, Indonesia
| | - Abdur Rahman Arif
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Hasanuddin University, Makassar, Indonesia
| | - Gita Syahputra
- Research Center for Biotechnology, Indonesian Institute of Science, Bogor, Indonesia
| | - Sukarti Sukarti
- Department of Chemistry, Faculty of Science, Universitas Cokroaminoto Palopo, Palopo, Indonesia
| | - Isman Kurniawan
- School of Computing, Telkom University, Bandung, Indonesia
- Research Center of Human Centric Engineering, Telkom University, Bandung, Indonesia
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Abdullahi M, Adeniji SE, Arthur DE, Haruna A. Homology modeling and molecular docking simulation of some novel imidazo[1,2-a]pyridine-3-carboxamide (IPA) series as inhibitors of Mycobacterium tuberculosis. J Genet Eng Biotechnol 2021; 19:12. [PMID: 33474593 PMCID: PMC7817721 DOI: 10.1186/s43141-020-00102-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/07/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND Tuberculosis (TB) remains a serious global health challenge that is caused by Mycobacterium tuberculosis and has killed numerous people. This necessitated the urgent need for the hunt and development of more potent drugs against the fast-emerging extensively drug-resistant (XDR) and multiple-drug-resistant (MDR) M. tuberculosis strains. Mycobacterium tuberculosis cytochrome b subunit of the cytochrome bc1 complex (QcrB) was recognized as a potential drug target in M. tuberculosis (25618/H37Rv) for imidazo[1,2-a]pyridine-3-carboxamides whose crystal strucuture is not yet reported in the Protein Data Bank (PDB). The concept of homology modeling as a powerful and useful computational method can be applied, since the M. tuberculosis QcrB protein sequence data are available. RESULTS The homology model of QcrB protein in M. tuberculosis was built from the X-ray structure of QcrB in M. smegmatis as a template using the Swiss-Model online workspace. The modeled protein was assessed, validated, and prepared for the molecular docking simulation of 35 ligands of N-(2-phenoxy)ethyl imidazo[1,2-a] pyridine-3-carboxamide (IPA) to analyze their theoretical binding affinities and modes. The docking results showed that the binding affinity values ranged from - 6.5 to - 10.1 kcal/mol which confirms their resilience potency when compared with 6.0kcal/mol of isoniazid standard drug. However, ligands 2, 7, 22, 26, and 35 scored higher binding affinity values of - 9.60, - 9.80, - 10.10, - 10.00, and - 10.00 kcal/mol, and are respectively considered as the best ligands among others with better binding modes in the active site of the modeled QcrB protein. CONCLUSION The information derived in this research revealed some potential hits and paved a route for structure-based drug discovery of new hypothetical imidazo pyridine amide analogs as anti-tubercular drug candidates.
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Affiliation(s)
- Mustapha Abdullahi
- Faculty of Physical sciences, Department of Chemistry, Ahmadu Bello University, P.M.B. 1044, Kaduna State Zaria, Federal Republic of Nigeria
| | - Shola Elijah Adeniji
- Faculty of Physical sciences, Department of Chemistry, Ahmadu Bello University, P.M.B. 1044, Kaduna State Zaria, Federal Republic of Nigeria
| | | | - Abdurrashid Haruna
- Faculty of Physical sciences, Department of Chemistry, Ahmadu Bello University, P.M.B. 1044, Kaduna State Zaria, Federal Republic of Nigeria
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Abdullahi M, Adeniji SE. In-silico Molecular Docking and ADME/Pharmacokinetic Prediction Studies of Some Novel Carboxamide Derivatives as Anti-tubercular Agents. CHEMISTRY AFRICA 2020. [DOI: 10.1007/s42250-020-00162-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractMolecular docking simulation of thirty-five (35) molecules of N-(2-phenoxy)ethyl imidazo[1,2-a]pyridine-3-carboxamide (IPA) with Mycobacterium tuberculosis target (DNA gyrase) was carried out so as to evaluate their theoretical binding affinities. The chemical structure of the molecules was accurately drawn using ChemDraw Ultra software, then optimized at density functional theory (DFT) using Becke’s three-parameter Lee–Yang–Parr hybrid functional (B3LYP/6-311**) basis set in a vacuum of Spartan 14 software. Subsequently, the docking operation was carried out using PyRx virtual screening software. Molecule 35 (M35) with the highest binding affinity of − 7.2 kcal/mol was selected as the lead molecule for structural modification which led to the development of four (4) newly hypothetical molecules D1, D2, D3 and D4. In addition, the D4 molecule with the highest binding affinity value of − 9.4 kcal/mol formed more H-bond interactions signifying better orientation of the ligand in the binding site compared to M35 and isoniazid standard drug. In-silico ADME and drug-likeness prediction of the molecules showed good pharmacokinetic properties having high gastrointestinal absorption, orally bioavailable, and less toxic. The outcome of the present research strengthens the relevance of these compounds as promising lead candidates for the treatment of multidrug-resistant tuberculosis which could help the medicinal chemists and pharmaceutical professionals in further designing and synthesis of more potent drug candidates. Moreover, the research also encouraged the in vivo and in vitro evaluation study for the proposed designed compounds to validate the computational findings.
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