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Oladipo SD, Zamisa SJ, Badeji AA, Ejalonibu MA, Adeleke AA, Lawal IA, Henni A, Lawal MM. Ni 2+ and Cu 2+ complexes of N-(2,6-dichlorophenyl)-N-mesityl formamidine dithiocarbamate structural and functional properties as CYP3A4 potential substrates. Sci Rep 2023; 13:13414. [PMID: 37591990 PMCID: PMC10435461 DOI: 10.1038/s41598-023-39502-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/26/2023] [Indexed: 08/19/2023] Open
Abstract
Metal compounds continued to attract diverse applications due to their malleability in several capacities. In this study, we present our findings on the crystal structures and functional properties of Ni2+ and Cu2+ complexes of N'-(2,6-dichlorophenyl)-N-mesitylformamidine dithiocarbamate (L) comprising [Ni-(L)2] (1) and [Cu-(L)2] (2) with a four-coordinate metal center. We established the two complex structures through 1H and 13C nuclear magnetic resonance (NMR), elemental, and single-crystal X-ray analysis. The analyses showed that the two complexes are isomorphous, having P21/c as a space group and a unit-cell similarity index (π) of 0.002. The two complexes conform to a distorted square planar geometry around the metal centers. The calculated and experimental data, including bond lengths, angles, and NMR values, are similar. Hirshfeld surface analysis revealed the variational contribution of the different types of intermolecular contacts driven by the crystal lattice of the two solvated complexes. Our knowledge of the potential biological implication of these structures enabled us to probe the compounds as prospective CYP3A4 inhibitors. This approach mimics current trends in pharmaceutical design and biomedicine by incorporating potentially active molecules into various media to predict their biological efficacies. The simulations show appreciable binding of compounds 1 and 2 to CYP3A4 with average interaction energies of -97 and -87 kcal/mol, respectively. The protein attains at least five conformational states in the three studied models using a Gaussian Mixture Model-based clustering and free energy prediction. Electric field analysis shows the crucial residues to substrate binding at the active site, enabling CYP3A4 structure to function prediction. The predicted inhibition with these Ni2+ and Cu2+ complexes indicates that CYP3A4 overexpression in a diseased state like cancer would reduce, thereby increasing the chemotherapeutic compounds' shelf-lives for adsorption. This multidimensional study addresses various aspects of molecular metal electronics, including their application as substrate-mimicking inhibitors. The outcome would enable further research on bio-metal compounds of critical potential.
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Affiliation(s)
- Segun D Oladipo
- Department of Chemical Sciences, Olabisi Onabanjo University, P.M.B 2002, Ago-Iwoye, Nigeria.
- School of Chemistry and Physics, Westville Campus, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa.
| | - Sizwe J Zamisa
- School of Chemistry and Physics, Westville Campus, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa
| | - Abosede A Badeji
- Department of Chemical Sciences, Tai Solarin University of Education, Ogun State, Ijagun, Nigeria
| | - Murtala A Ejalonibu
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa
| | - Adesola A Adeleke
- Department of Chemical Sciences, Olabisi Onabanjo University, P.M.B 2002, Ago-Iwoye, Nigeria
| | - Isiaka A Lawal
- Faculty of Engineering and Applied Science, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2, Canada
| | - Amr Henni
- Faculty of Engineering and Applied Science, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2, Canada
| | - Monsurat M Lawal
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa.
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Akinyele OF, Fakola EG, Adeboye OO, Chinuomah SC. Investigation of Methyl-5-(pentan-3-yloxy)-7-oxabicyclo[4.1.0]hept-3-ene-3-carboxyhydrazide Derivatives as Potential Inhibitors of COVID-19 Main Protease: DFT and Molecular Docking Study. Bioinform Biol Insights 2023; 17:11779322231182050. [PMID: 37377795 PMCID: PMC10291222 DOI: 10.1177/11779322231182050] [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: 01/31/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
The search for effective therapeutics to combat COVID-19 has led to the exploration of the biological activity of numerous compounds. In this study, hydrazones derived from oseltamivir intermediate, methyl 5-(pentan-3-yloxy)-7-oxabicyclo[4.1.0]hept-3-ene-3-carboxylate have been investigated for their potential as drug candidates against the COVID-19 virus using computational methods, including density functional theory (DFT) studies, molecular docking, and absorption, distribution, metabolism, excretion and toxicity (ADMET) analysis. The DFT studies provide information on the electronic properties of the compounds while the molecular docking results using AutoDock reported the binding energies between the main protease of COVID-19 and the compounds. The DFT results revealed that the energy gap of the compounds ranged from 4.32 to 5.82 eV while compound HC had the highest energy gap (5.82 eV) and chemical potential (2.90 eV). The electrophilicity index values of the 11 compounds ranged from 2.49 to 3.86, thus they were classified as strong electrophiles. The molecular electrostatic potential (MESP) revealed electron-rich and electron-deficient regions of the compounds. The docking results reveal that all the compounds had better docking scores than remdesivir and chloroquine, frontline drugs employed in combating COVID-19, with HC having the best docking score of -6.5. The results were visualized using Discovery studio, which revealed hydrogen bonding, pi-alkyl interaction, alkyl interaction, salt bridge interaction, halogen interaction as being responsible for the docking scores. The drug-likeness results showed that the compounds qualify as oral drug candidates as none of them violated Vebers and Lipinski's rule. Thus, they could serve as potential inhibitors of COVID-19.
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Sharma H, Raju B, Narendra G, Kumar M, Verma H, Sharma B, Tung GK, Kumar Jain S, Brás NF, Silakari O. In silico guided designing of optimized benzochalcones derivatives as potent CYP1B1 inhibitors: An integrated in vitro and ONIOM study. J Mol Graph Model 2023; 119:108390. [PMID: 36502606 DOI: 10.1016/j.jmgm.2022.108390] [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: 10/19/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022]
Abstract
Cytochrome P4501B1 (CYP1B1) is reported to be overexpressed in various malignancies including ovarian, lung, lymph, and breast cancers. The overexpression of this enzyme is accountable for the biotransformation-based inactivation of some anti-cancer drugs i.e. Docetaxel, Paclitaxel, and Cisplatin. To circumvent solutions to this issue, the current study reports some optimized derivatives of benzochalcone as selective CYP1B1 inhibitors. The optimized derivatives were screened using some structure-based drug-designing approaches including molecular docking and molecular dynamics. The implemented approaches revealed that all the designed molecules demonstrated not only essential interactions with key amino acid residues but also maintained stability within the active site of CYP1B1. Furthermore, to validate the in-silico results and develop a SAR, the designed molecules were subsequently synthesized and tested for their ability to selectively inhibit CYP1B1 over CYP1A1 using well established EROD assay. This assay results suggested that compounds 1(c), 1(d), and 1(e) are eightfold more selective CYP1B1 inhibitors over CYP1A1 with IC50 values ranging from 0.06 to 0.09 μM respectively. Among these, compound 1(d) manifested potent inhibitory activity i.e. IC50 of 0.06 μM with 24 folds selectivity over 1A1. To have a better insight into the binding pattern of 1(d) within CYP1B1 and precisely compute binding affinity for 1(d)-CYP1B1 complex, one of the advanced QM/MM approaches i.e. ONIOM has been implemented. Where 1(d)-CYP1B1 complex conferred comparable binding affinity in terms of ΔG (kcal/mol) with that of ANF-CYP1B1 complex. This research could provide a suitable starting point for the development of more potent multi-functional compounds with CYP1B1 inhibitory activity.
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Affiliation(s)
- Himani Sharma
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Baddipadige Raju
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Gera Narendra
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Manoj Kumar
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Himanshu Verma
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Bhavna Sharma
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Gurleen Kaur Tung
- Center for Basic and Translational Research in Health Sciences, Guru Nanak Dev University, Amritsar, India
| | - Subheet Kumar Jain
- Center for Basic and Translational Research in Health Sciences, Guru Nanak Dev University, Amritsar, India
| | - Natércia F Brás
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Om Silakari
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India.
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Mishma J, Jothy V, Irfan A, Narayana B, Kodlady SN, Muthu S. Solvent potential effects (topological aspects, electron excitation), Spectral characterization and biological attributes of NLO active 1-(2,4Dinitrophenyl)-2-((E)-3-phenylallylidene) hydrazine: Multiple anti tuberculosis agent. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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Singh A, Kumar S, Gupta VK, Singh S, Dwivedi VD, Mina U. Computational assessment of Withania somnifera phytomolecules as putative inhibitors of Mycobacterium tuberculosis CTP synthase PyrG. J Biomol Struct Dyn 2022:1-14. [PMID: 35549811 DOI: 10.1080/07391102.2022.2074142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Genome evolution of Mycobacterium tuberculosis (Mtb) produces new strains resistant to various pre-existing anti-tubercular drugs. Hence, there is an urgent need to explore potent compounds with the most negligible side effects and effective Mtb inhibition. Mtb PyrG (CTP synthase) is a crucial enzyme for the conversion of the uridine triphosphate (UTP) into cytidine triphosphate (CTP) and is essential for the growth of Mtb. Thus, in this study, phytochemicals of Withania somnifera (W. somnifera) were screened to find the potential inhibitors against Mtb PyrG. Molecular docking resulted in the identification of quercetin 3-rutinoside-7-glucoside, rutin, chlorogenic acid and isochlorogenic acid C with a substantial docking score (from -12.6 to -10.8 kcal/mol) contributed by significant intermolecular interactions. Furthermore, 100 ns molecular dynamics simulation, ADME analysis and free binding energy calculations support the stability of docked complexes and drug-likeness for selected compounds, respectively. Collectively, these findings suggest that phytochemicals present in W. somnifera can be considered for further evaluation against Mtb in a series of in vitro and in vivo models.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ankita Singh
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sanjay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Vivek Kumar Gupta
- ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, India
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Vivek Dhar Dwivedi
- Centre for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Usha Mina
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
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6
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Ejalonibu MA, Elrashedy AA, Lawal MM, Mhlongo NN, Kumalo HM. Pharmacophore mapping of the crucial mediators of dual inhibitor activity of PanK and PyrG in tuberculosis disease. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.2019251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Murtala A. Ejalonibu
- Biomolecular Modeling Research Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Ahmed A. Elrashedy
- Natural and Microbial Product Department, National Research Centre, Giza, Egypt
| | - Monsurat M. Lawal
- Biomolecular Modeling Research Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Ndumiso N. Mhlongo
- Biomolecular Modeling Research Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Hezekiel M. Kumalo
- Biomolecular Modeling Research Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
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Drug Discovery for Mycobacterium tuberculosis Using Structure-Based Computer-Aided Drug Design Approach. Int J Mol Sci 2021; 22:ijms222413259. [PMID: 34948055 PMCID: PMC8703488 DOI: 10.3390/ijms222413259] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/09/2021] [Accepted: 11/14/2021] [Indexed: 12/12/2022] Open
Abstract
Developing new, more effective antibiotics against resistant Mycobacterium tuberculosis that inhibit its essential proteins is an appealing strategy for combating the global tuberculosis (TB) epidemic. Finding a compound that can target a particular cavity in a protein and interrupt its enzymatic activity is the crucial objective of drug design and discovery. Such a compound is then subjected to different tests, including clinical trials, to study its effectiveness against the pathogen in the host. In recent times, new techniques, which involve computational and analytical methods, enhanced the chances of drug development, as opposed to traditional drug design methods, which are laborious and time-consuming. The computational techniques in drug design have been improved with a new generation of software used to develop and optimize active compounds that can be used in future chemotherapeutic development to combat global tuberculosis resistance. This review provides an overview of the evolution of tuberculosis resistance, existing drug management, and the design of new anti-tuberculosis drugs developed based on the contributions of computational techniques. Also, we show an appraisal of available software and databases on computational drug design with an insight into the application of this software and databases in the development of anti-tubercular drugs. The review features a perspective involving machine learning, artificial intelligence, quantum computing, and CRISPR combination with available computational techniques as a prospective pathway to design new anti-tubercular drugs to combat resistant tuberculosis.
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8
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Adeowo FY, Oyetunji TP, Ejalonibu MA, Ndagi U, Kumalo HM, Lawal MM. Tailored Modeling of Rivastigmine Derivatives as Dual Acetylcholinesterase and Butyrylcholinesterase Inhibitors for Alzheimer's Disease Treatment. Chem Biodivers 2021; 18:e2100361. [PMID: 34547176 DOI: 10.1002/cbdv.202100361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/21/2021] [Indexed: 12/13/2022]
Abstract
Rational modification of known drug candidates to design more potent ones using computational methods has found application in drug design, development, and discovery. Herein, we integrate computational and theoretical methodologies to unveil rivastigmine derivatives as dual inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) for Alzheimer's disease (AD) management. The investigation entails pharmacokinetics screening, density functional theory (DFT) mechanistic study, molecular docking, and molecular dynamics (MD) simulation. We designed over 20 rivastigmine substituents, subject them to some analyses, and identified RL2 with an appreciable blood-brain barrier score and no permeability glycoprotein binding. The compound shows higher acylation energy and a favored binding affinity to the cholinesterase enzymes. RL2 interacts with the AChE and BuChE active sites showing values of -41.1/-39.5 kcal mol-1 while rivastigmine binds with -32.7/-30.7 kcal mol-1 for these enzymes. The study revealed RL2 (4-fluorophenyl rivastigmine) as a potential dual inhibitor for AChE and BuChE towards Alzheimer's disorder management.
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Affiliation(s)
- Fatima Y Adeowo
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, 4001, South Africa
| | | | - Murtala A Ejalonibu
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Umar Ndagi
- Center for Trans-Sahara Disease, Vaccine and Drug Research, IBB University Lapai, Niger State, Minna, Nigeria
| | - Hezekiel M Kumalo
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Monsurat M Lawal
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, 4001, South Africa
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9
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Yusuf T, Oladipo SD, Zamisa S, Kumalo HM, Lawal IA, Lawal MM, Mabuba N. Design of New Schiff-Base Copper(II) Complexes: Synthesis, Crystal Structures, DFT Study, and Binding Potency toward Cytochrome P450 3A4. ACS OMEGA 2021; 6:13704-13718. [PMID: 34095663 PMCID: PMC8173565 DOI: 10.1021/acsomega.1c00906] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/07/2021] [Indexed: 06/01/2023]
Abstract
We report the synthesis and crystal structures of three new copper(II) Schiff-base complexes. The complexes have been characterized by elemental analysis and Fourier transform infrared (FT-IR) and UV-visible spectroscopies. The X-ray diffraction (XRD) analysis reveals that complexes 1 and 3 crystallize in a monoclinic space group C2/c and 2 in a triclinic space group P1̅, each adopting a square planar geometry around the metal center. We use a density functional theory method to explore the quantum chemical properties of these complexes. The calculation proceeds with the three-dimensional (3D) crystal structure characterization of the complexes in which the calculated IR and UV-vis values are comparable to the experimental results. Charge distribution and molecular orbital analyses enabled quantum chemical property prediction of these complexes. We study the drug-likeness properties and binding potentials of the synthesized complexes. The in silico outcome showed that they could serve as permeability-glycoprotein (P-gp) and different cytochrome P450 substrates. Our calculations showed that the complexes significantly bind to cytochrome P450 3A4.
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Affiliation(s)
- Tunde
L. Yusuf
- Department
of Chemical Sciences, University of Johannesburg, Doornfontein, P.O.
Box 17011, Johannesburg 2028, South Africa
| | - Segun D. Oladipo
- Department
of Chemical Sciences, Olabisi Onabanjo University, P. M. B., 2002 Ago-Iwoye, Nigeria
| | - Sizwe Zamisa
- School
of Chemistry and Physics, University of
KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa
| | - Hezekiel M. Kumalo
- Discipline
of Medical Biochemistry, School of Laboratory Medicine and Medical
Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South
Africa
| | - Isiaka A. Lawal
- Chemistry
Department, Faculty of Applied and Computer Science, Vaal University of Technology, Vanderbijlpark Campus, Boulevard, 1900 Vanderbijlpark, South Africa
| | - Monsurat M. Lawal
- Discipline
of Medical Biochemistry, School of Laboratory Medicine and Medical
Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South
Africa
| | - Nonhlangabezo Mabuba
- Department
of Chemical Sciences, University of Johannesburg, Doornfontein, P.O.
Box 17011, Johannesburg 2028, South Africa
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10
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Albuquerque ADO, da Silva Junior HC, Sartori GR, Martins da Silva JH. Computationally-obtained structural insights into the molecular interactions between Pidilizumab and binding partners DLL1 and PD-1. J Biomol Struct Dyn 2021; 40:6450-6462. [PMID: 33559526 DOI: 10.1080/07391102.2021.1885492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Pidilizumab is a monoclonal antibody tested against several types of malignancies, such as lymphoma and metastatic melanoma, showing promising results. In 2016, the FDA put Pidilizumab's clinical studies on partial hold due to emerging evidence pointing to the antibody target uncertainty. Although initial studies indicated an interaction with the PD-1 checkpoint receptor, recent updates assert that Pidilizumab binds primarily to Notch ligand DLL1. However, a detailed description of which interactions coordinate antibody-antigen complex formation is lacking. Therefore, this study uses computational tools to identify molecular interactions between Pidilizumab and its reported targets PD-1 and DLL1. A docking methodology was validated and applied to determine the binding modes between modeled Pidilizumab scFvs and the two antigens. We used Molecular Dynamics (MD) simulations to verify the complexes' stability and submitted the resulting trajectory files to MM/PBSA and Principal Component Analysis. A set of different prediction tools determined scFv interface hot-spots. Whereas docking and MD simulations revealed that the antibody fragments do not interact straightforwardly with PD-1, ten scFv hot-spots, including Met93 and Leu112, mediated the interaction with the DLL1 C2 domain. The interaction triggered a conformational selection-like effect on DLL1, allowing new hydrogen bonds on the β3-β4 interface loop. The unprecedented structural data on Pidilizumab's interactions provided novel evidence that its legitimate target is the DLL1 protein and offered structural insight on how these molecules interact, shedding light on the pathways that could be affected by the use of this essential immunobiological.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Geraldo Rodrigues Sartori
- Grupo para Modelagem, Simulação e Evolução, in sílico, de Biomoléculas, Fiocruz-Ceará, Eusébio, Brazil
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11
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Akinpelu OI, Lawal MM, Kumalo HM, Mhlongo NN. Computational studies of the properties and activities of selected trisubstituted benzimidazoles as potential antitubercular drugs inhibiting MTB-FtsZ polymerization. J Biomol Struct Dyn 2020; 40:1558-1570. [PMID: 33021149 DOI: 10.1080/07391102.2020.1830176] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Trisubstituted benzimidazoles (trisbenz) are significantly active against nonreplicating Mycobacterium tuberculosis (MTB) by inhibiting the polymerization of Filamentous Temperature Sensitive Mutant Z (FtsZ), an essential bacteria cell division protein. In-depth in-silico study of 5 of the most active trisubstituted benzimidazoles; trisbenz 1, 2, 3, 4 and 5, giving insight into their properties, such as stability, bioavailability, interactions with residues at the binding site of MTB-FtsZ and their influence on structural dynamics of the protein have been conducted. This was achieved through the application of in-silico methods including density functional theory (DFT) calculations, ADME properties calculations, molecular docking and molecular dynamics simulations. A DFT approach was applied to predict reactivity properties of potent FtsZ inhibitors, and the results reveal the relative reactivity of these inhibitors as bioactive moieties. The estimated ADME properties predicted all 5 compounds to be bioavailable and suitable for oral administration. Molecular docking, binding free energy, RMSD, RMSF, and hydrogen bond analysis confirmed these 5 compounds as potent MTB-FtsZ inhibitors. Although analyses proved these compounds to be bioactive and potent MTB-FtsZ inhibitors, however, trisbenz 1 appeared to be the most active against this protein while trisbenz 5 was the least active. This study further confirms the experimental study while also giving insight on the compounds mechanism of action and presents their bioavailability properties.
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Affiliation(s)
- Olayinka I Akinpelu
- Biomolecular Modelling Research Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa.,School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Monsurat M Lawal
- Biomolecular Modelling Research Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Hezekiel M Kumalo
- Biomolecular Modelling Research Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Ndumiso N Mhlongo
- Biomolecular Modelling Research Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
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12
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Magwenyane AM, Mhlongo NN, Lawal MM, Amoako DG, Somboro AM, Sosibo SC, Shunmugam L, Khan RB, Kumalo HM. Understanding the Hsp90 N-terminal Dynamics: Structural and Molecular Insights into the Therapeutic Activities of Anticancer Inhibitors Radicicol (RD) and Radicicol Derivative (NVP-YUA922). Molecules 2020; 25:E1785. [PMID: 32295059 PMCID: PMC7221724 DOI: 10.3390/molecules25081785] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/03/2020] [Accepted: 04/08/2020] [Indexed: 11/23/2022] Open
Abstract
Heat shock protein 90 (Hsp90) is a crucial component in carcinogenesis and serves as a molecular chaperone that facilitates protein maturation whilst protecting cells against temperature-induced stress. The function of Hsp90 is highly dependent on adenosine triphosphate (ATP) binding to the N-terminal domain of the protein. Thus, inhibition through displacement of ATP by means of competitive binding with a suitable organic molecule is considered an attractive topic in cancer research. Radicicol (RD) and its derivative, resorcinylic isoxazole amine NVP-AUY922 (NVP), have shown promising pharmacodynamics against Hsp90 activity. To date, the underlying binding mechanism of RD and NVP has not yet been investigated. In this study, we provide a comprehensive understanding of the binding mechanism of RD and NVP, from an atomistic perspective. Density functional theory (DFT) calculations enabled the analyses of the compounds' electronic properties and results obtained proved to be significant in which NVP was predicted to be more favorable with solvation free energy value of -23.3 kcal/mol and highest stability energy of 75.5 kcal/mol for a major atomic delocalization. Molecular dynamic (MD) analysis revealed NVP bound to Hsp90 (NT-NVP) is more stable in comparison to RD (NT-RD). The Hsp90 protein exhibited a greater binding affinity for NT-NVP (-49.4 ± 3.9 kcal/mol) relative to NT-RD (-28.9 ± 4.5 kcal/mol). The key residues influential in this interaction are Gly 97, Asp 93 and Thr 184. These findings provide valuable insights into the Hsp90 dynamics and will serve as a guide for the design of potent novel inhibitors for cancer treatment.
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Affiliation(s)
- Ayanda M. Magwenyane
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
| | - Ndumiso N. Mhlongo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
| | - Monsurat M. Lawal
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
| | - Daniel G. Amoako
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
- Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Anou M. Somboro
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
- Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Sphelele C. Sosibo
- School of Physical and Chemical Sciences, Department of Chemistry, North West University, Mafikeng Campus, Mmabatho 2790, South Africa;
| | - Letitia Shunmugam
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
| | - Rene B. Khan
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
| | - Hezekiel M. Kumalo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
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