1
|
Awoonor-Williams E, Abu-Saleh AAAA. Molecular Insights into the Impact of Mutations on the Binding Affinity of Targeted Covalent Inhibitors of BTK. J Phys Chem B 2024; 128:2874-2884. [PMID: 38502552 DOI: 10.1021/acs.jpcb.4c00310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Targeted covalent inhibitors (TCIs) have witnessed a significant resurgence in recent years, particularly in the kinase drug discovery field for treating diverse clinical indications. The inhibition of Bruton's tyrosine kinase (BTK) for treating B-cell cancers is a classic example where TCIs such as ibrutinib have had breakthroughs in targeted therapy. However, selectivity remains challenging, and the emergence of resistance mutations is a critical concern for clinical efficacy. Computational methods that can accurately predict the impact of mutations on inhibitor binding affinity could prove helpful in informing targeted approaches─providing insights into drug resistance mechanisms. In addition, such systems could help guide the systematic evaluation and impact of mutations in disease models for optimal experimental design. Here, we have employed in silico physics-based methods to understand the effects of mutations on the binding affinity and conformational dynamics of select TCIs of BTK. The TCIs studied include ibrutinib, acalabrutinib, and zanubrutinib─all of which are FDA-approved drugs for treating multiple forms of leukemia and lymphoma. Our results offer useful molecular insights into the structural determinants, thermodynamics, and conformational energies that impact ligand binding for this biological target of clinical relevance.
Collapse
Affiliation(s)
- Ernest Awoonor-Williams
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL A1B 3X7, Canada
| | - Abd Al-Aziz A Abu-Saleh
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| |
Collapse
|
2
|
Al-Hawarin JI, Abu-Yamin AA, Abu-Saleh AAAA, Saraireh IAM, Almatarneh MH, Hasan M, Atrooz OM, Al-Douri Y. Synthesis, Characterization, and DFT Calculations of a New Sulfamethoxazole Schiff Base and Its Metal Complexes. Materials (Basel) 2023; 16:5160. [PMID: 37512433 PMCID: PMC10385116 DOI: 10.3390/ma16145160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023]
Abstract
A new Schiff base, 4-((1E,2E)-3-(furan-2-yl)allylidene)amino)-N-(5-methylisoxazol-3-yl) benzene-sulfonamide (L), was synthesized by thermal condensation of 3-(2-furyl)acrolein and sulfamethoxazole (SMX), and the furan Schiff base (L) was converted to a phenol Schiff base (L') according to the Diels-Alder [4 + 2] cycloaddition reaction and studied experimentally. The structural and spectroscopic properties of the Schiff base were also corroborated by utilizing density functional theory (DFT) calculations. Furthermore, a series of lanthanide and transition metal complexes of the Schiff base were synthesized from the nitrate salts of Gd, Sm, Nd, and Zn (L1, L2, L3, and L4), respectively. Various spectroscopic studies confirmed the chemical structures of the Schiff-base ligand and its complexes. Based on the spectral studies, a nine-coordinated geometry was assigned to the lanthanide complexes and a six-coordinated geometry to the zinc complex. The elemental analysis data confirmed the suggested structure of the metal complexes, and the TGA studies confirmed the presence of one coordinated water molecule in the lanthanide complexes and one crystalline water molecule in the zinc complex; in addition, the conductivity showed the neutral nature of the complexes. Therefore, it is suggested that the ligand acts as a bidentate through coordinates to each metal atom by the isoxazole nitrogen and oxygen atoms of the sulfur dioxide moiety of the SMX based on FTIR studies. The ligand and its complexes were tested for their anti-inflammatory, anti-hemolytic, and antioxidant activities by various colorimetric methods. These complexes were found to exhibit potential effects of the selected biological activities.
Collapse
Affiliation(s)
- Jibril I Al-Hawarin
- Department of Chemistry, Al-Hussein Bin Talal University, Ma'an 71111, Jordan
| | | | | | | | - Mansour H Almatarneh
- Department of Chemistry, Memorial University, St. John's, NL A1B 3X7, Canada
- Department of Chemistry, University of Jordan, Amman 11942, Jordan
| | - Mahmood Hasan
- Hepi Company (Home of Experience) for Paints and Inks, Cairo 61710, Egypt
| | - Omar M Atrooz
- Department of Biological Sciences, Mutah University, Mutah 617102, Jordan
| | - Y Al-Douri
- Nanotechnology and Catalysis Research Center (NANOCAT), University of Malaya, Kuala Lumpur 50603, Malaysia
- Department of Mechanical Engineering, Faculty of Engineering, Piri Reis University, Eflatun Sk. No: 8, Istanbul 34940, Tuzla, Turkey
- Department of Applied Physics and Astronomy, College of Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| |
Collapse
|
3
|
Ali Z, Kaur S, Kukhta T, Abu-Saleh AAAA, Jhunjhunwala A, Mitra A, Trant JF, Sharma P. Structural Mapping of the Base Stacks Containing Post-transcriptionally Modified Bases in RNA. J Phys Chem B 2023. [PMID: 37369074 DOI: 10.1021/acs.jpcb.3c02268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Post-transcriptionally modified bases play vital roles in many biochemical processes involving RNA. Analysis of the non-covalent interactions associated with these bases in RNA is crucial for providing a more complete understanding of the RNA structure and function; however, the characterization of these interactions remains understudied. To address this limitation, we present a comprehensive analysis of base stacks involving all crystallographic occurrences of the most biologically relevant modified bases in a large dataset of high-resolution RNA crystal structures. This is accompanied by a geometrical classification of the stacking contacts using our established tools. Coupled with quantum chemical calculations and an analysis of the specific structural context of these stacks, this provides a map of the stacking conformations available to modified bases in RNA. Overall, our analysis is expected to facilitate structural research on altered RNA bases.
Collapse
Affiliation(s)
- Zakir Ali
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Sarabjeet Kaur
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
- Surface Chemistry and Catalysis: Characterisation and Application Team (COK-KAT), Leuven (Arenberg) Celestijnenlaan 200f─Box 2461, 3001 Leuven, Belgium
| | - Teagan Kukhta
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
| | - Abd Al-Aziz A Abu-Saleh
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
- Binary Star Research Services, LaSalle, Ontario N9J 3X8, Canada
| | - Ayush Jhunjhunwala
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad, Telangana 500032, India
| | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad, Telangana 500032, India
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
- Binary Star Research Services, LaSalle, Ontario N9J 3X8, Canada
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
| |
Collapse
|
4
|
Abu-Saleh AAAA, Yadav A, Poirier RA. Accelerating the discovery of the beyond rule of five compounds that have high affinities toward SARS-CoV-2 spike RBD. J Biomol Struct Dyn 2022; 41:2518-2527. [PMID: 35132950 DOI: 10.1080/07391102.2022.2036640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The battle against SARS-CoV-2 coronavirus is the focal point for the global pandemic that has affected millions of lives worldwide. The need for effective and selective therapeutics for the treatment of the disease caused by SARS-CoV-2 is critical. Herein, we performed a hierarchical computational approach incorporating molecular docking studies, molecular dynamics simulations, absolute binding energy calculations, and steered molecular dynamics simulations for the discovery of potential compounds with high affinity towards SARS-CoV-2 spike RBD. By leveraging ZINC15 database, a total of 1282 in-clinical and FDA approved drugs were filtered out from nearly 0.5 million protomers of relatively large compounds (MW > 500, and LogP ≤ 5). Our results depict plausible mechanistic aspects related to the blockage of SARS-CoV-2 spike RBD by the top hits discovered. We found that the most promising candidates, namely, ZINC95628821, ZINC95617623, ZINC3979524, and ZINC261494658, strongly bind to the spike RBD and interfere with the human ACE2 receptor. These findings accelerate the rational design of selective inhibitors targeting the spike RBD protein of SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | - Arpita Yadav
- Department of Chemistry, University Institute of Engineering & Technology, Chhatrapati Shahu Ji Maharaj University, Kanpur, India
| | | |
Collapse
|
5
|
Awoonor-Williams E, Abu-Saleh AAAA. Covalent and non-covalent binding free energy calculations for peptidomimetic inhibitors of SARS-CoV-2 main protease. Phys Chem Chem Phys 2021; 23:6746-6757. [PMID: 33711090 DOI: 10.1039/d1cp00266j] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
COVID-19, the disease caused by the newly discovered coronavirus-SARS-CoV-2, has created a global health, social, and economic crisis. As of mid-January 2021, there are over 90 million confirmed cases and more than 2 million reported deaths due to COVID-19. Currently, there are very limited therapeutics for the treatment or prevention of COVID-19. For this reason, it is important to find drug targets that will lead to the development of safe and effective therapeutics against the disease. The main protease (Mpro) of the virus is an attractive target for the development of effective antiviral therapeutics because it is required for proteolytic cleavage of viral polyproteins. Furthermore, the Mpro has no human homologues, so drugs designed to bind to this target directly have less risk for off-target effects. Recently, several high-resolution crystallographic structures of the Mpro in complex with inhibitors have been determined-to guide drug development and to spur efforts in structure-based drug design. One of the primary objectives of modern structure-based drug design is the accurate prediction of receptor-ligand binding affinities for rational drug design and discovery. Here, we perform rigorous alchemical absolute binding free energy calculations and QM/MM calculations to give insight into the total binding energy of two recently crystallized inhibitors of SARS-CoV-2 Mpro, namely, N3 and α-ketoamide 13b. The total binding energy consists of both covalent and non-covalent binding components since both compounds are covalent inhibitors of the Mpro. Our results indicate that the covalent and non-covalent binding free energy contributions of both inhibitors to the Mpro target differ significantly. The N3 inhibitor has more favourable non-covalent interactions, particularly hydrogen bonding, in the binding site of the Mpro than the α-ketoamide inhibitor. Also, the Gibbs energy of reaction for the Mpro-N3 covalent adduct is greater than the Gibbs reaction energy for the Mpro-α-ketoamide covalent adduct. These differences in the covalent and non-covalent binding free energy contributions for both inhibitors could be a plausible explanation for their in vitro differences in antiviral activity. Our findings are consistent with the reversible and irreversible character of both inhibitors as reported by experiment and highlight the importance of both covalent and non-covalent binding free energy contributions to the absolute binding affinity of a covalent inhibitor towards its target. This information could prove useful in the rational design, discovery, and evaluation of potent SARS-CoV-2 Mpro inhibitors for targeted antiviral therapy.
Collapse
Affiliation(s)
- Ernest Awoonor-Williams
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
| | | |
Collapse
|
6
|
Awoonor-williams E, Abu-saleh AAA. Covalent and Non-Covalent Binding Free Energy Calculations for Peptidomimetic Inhibitors of SARS-CoV-2 Main Protease.. [DOI: 10.26434/chemrxiv.13288463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
COVID-19, the disease caused by the newly discovered coronavirus — SARS-CoV-2, has created global health, social, and economic crisis. At the time of writing (November 12, 2020), there are over 50 million confirmed cases and more than 1 million reported deaths due to COVID-19. Currently, there are no approved vaccines, and recently Veklury (remdesivir) was approved for the treatment of COVID-19 requiring hospitalization. The main protease (M<sup>pro</sup>) of the virus is an attractive target for the development of effective antiviral therapeutics because it is required for proteolytic cleavage of viral polyproteins. Furthermore, the M<sup>pro</sup> has no human homologues, so drugs designed to bind to this target directly have less risk for off-target reactivity. Recently, several high-resolution crystallographic structures of the M<sup>pro</sup> in complex with inhibitors have been determined — to guide drug development and to spur efforts in structure-based drug design. One of the primary objectives of modern structure-based drug design is the accurate prediction of receptor-ligand binding affinities for rational drug design and discovery. Here, we perform rigorous alchemical absolute binding free energy calculations and QM/MM calculations to give insight into the total binding energy of two recently crystallized inhibitors of SARS-CoV-2 M<sup>pro</sup>, namely, N3 and α-ketoamide 13b. The total binding energy consists of both covalent and non-covalent binding components since both compounds are covalent inhibitors of the M<sup>pro</sup>. Our results indicate that the covalent and non-covalent binding free energy contributions of both inhibitors to the M<sup>pro</sup> target differ significantly. The N3 inhibitor has more favourable non-covalent interactions, particularly hydrogen bonding, in the binding site of the M<sup>pro</sup> than the α-ketoamide inhibitor. But the Gibbs energy of reaction for the M<sup>pro</sup>–α-ketoamide covalent adduct is greater than the Gibbs reaction energy for the M<sup>pro</sup>–N3 covalent adduct. These differences in the covalent and non-covalent binding free energy contributions for both inhibitors could be a plausible explanation for their in vitro differences in antiviral activity. Our findings highlight the importance of both covalent and non-covalent binding free energy contributions to the absolute binding affinity of a covalent inhibitor towards its target.
Collapse
|
7
|
Awoonor-williams E, Abu-saleh AAA. Covalent and Non-Covalent Binding Free Energy Calculations for Peptidomimetic Inhibitors of SARS-CoV-2 Main Protease.. [DOI: 10.26434/chemrxiv.13288463.v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
COVID-19, the disease caused by the newly discovered coronavirus — SARS-CoV-2, has created global health, social, and economic crisis. At the time of writing (November 12, 2020), there are over 50 million confirmed cases and more than 1 million reported deaths due to COVID-19. Currently, there are no approved vaccines, and recently Veklury (remdesivir) was approved for the treatment of COVID-19 requiring hospitalization. The main protease (Mpro) of the virus is an attractive target for the development of effective antiviral therapeutics because it is required for proteolytic cleavage of viral polyproteins. Furthermore, the Mpro has no human homologues, so drugs designed to bind to this target directly have less risk for off-target reactivity. Recently, several high-resolution crystallographic structures of the Mpro in complex with inhibitors have been determined — to guide drug development and to spur efforts in structure-based drug design. One of the primary objectives of modern structure-based drug design is the accurate prediction of receptor-ligand binding affinities for rational drug design and discovery. Here, we perform rigorous alchemical absolute binding free energy calculations and QM/MM calculations to give insight into the total binding energy of two recently crystallized inhibitors of SARS-CoV-2 Mpro, namely, N3 and α-ketoamide 13b. The total binding energy consists of both covalent and non-covalent binding components since both compounds are covalent inhibitors of the Mpro. Our results indicate that the covalent and non-covalent binding free energy contributions of both inhibitors to the Mpro target differ significantly. The N3 inhibitor has more favourable non-covalent interactions, particularly hydrogen bonding, in the binding site of the Mpro than the α-ketoamide inhibitor. But the Gibbs energy of reaction for the Mpro–α-ketoamide covalent adduct is greater than the Gibbs reaction energy for the Mpro–N3 covalent adduct. These differences in the covalent and non-covalent binding free energy contributions for both inhibitors could be a plausible explanation for their in vitro differences in antiviral activity. Our findings highlight the importance of both covalent and non-covalent binding free energy contributions to the absolute binding affinity of a covalent inhibitor towards its target.
Collapse
|
8
|
Abu-Saleh AAAA, Awad IE, Yadav A, Poirier RA. Discovery of potent inhibitors for SARS-CoV-2's main protease by ligand-based/structure-based virtual screening, MD simulations, and binding energy calculations. Phys Chem Chem Phys 2020; 22:23099-23106. [PMID: 33025993 DOI: 10.1039/d0cp04326e] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
COVID-19 has caused lockdowns all over the world in early 2020, as a global pandemic. Both theoretical and experimental efforts are seeking to find an effective treatment to suppress the virus. In silico drug design can play a vital role in identifying promising drug candidates against COVID-19. Herein, we focused on the main protease of SARS-CoV-2 that has crucial biological functions in the virus. We performed a ligand-based virtual screening followed by a docking screening for testing approved drugs and bioactive compounds listed in the DrugBank and ChEMBL databases. The top 8 docking results were advanced to all-atom MD simulations to study the relative stability of the protein-ligand interactions. MD simulations support that the catalytic residue, His41, has a neutral side chain with a protonated delta position. An absolute binding energy (ΔG) of -42 kJ mol-1 for the protein-ligand (Mpro-N3) complex has been calculated using the potential-of-mean-force (geometrical) approach. Furthermore, the relative binding energies were computed for the top docking results. Our results suggest several promising approved and bioactive inhibitors of SARS-CoV-2 Mpro as follows: a bioactive compound, ChEMBL275592, which has the best MM/GBSA binding energy; the second-best compound, montelukast, is an approved drug used in the treatment of asthma and allergic rhinitis; the third-best compound, ChEMBL288347, is a bioactive compound. Bromocriptine and saquinavir are other approved drugs that also demonstrate stability in the active site of Mpro, albeit their relative binding energies are low compared to the N3 inhibitor. This study provides useful insights into de novo protein design and novel inhibitor development, which could reduce the cost and time required for the discovery of a potent drug to combat SARS-CoV-2.
Collapse
|
9
|
Awad IE, Abu-Saleh AAAA, Sharma S, Yadav A, Poirier RA. High-throughput virtual screening of drug databanks for potential inhibitors of SARS-CoV-2 spike glycoprotein. J Biomol Struct Dyn 2020; 40:2099-2112. [PMID: 33103586 PMCID: PMC7643424 DOI: 10.1080/07391102.2020.1835721] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
COVID-19, which is caused by a novel coronavirus known as SARS-CoV-2, has spread rapidly around the world, and it has infected more than 29 million individuals as recorded on 16 September 2020. Much effort has been made to stop the virus from spreading, and there are currently no approved pharmaceutical products to treat COVID-19. Here, we apply an in silico approach to investigate more than 3800 FDA approved drugs on the viral RBD S1-ACE2 interface as a target. The compounds were investigated through flexible ligand docking, ADME property calculations and protein–ligand interaction maps. Molecular dynamics (MD) simulations were also performed on eleven compounds to study the stability and the interactions of the protein–ligand complexes. The MD simulations show that bagrosin, chidamide, ebastine, indacaterol, regorafenib, salazosulfadimidine, silodosin and tasosartan are relatively stable near the C terminal domain (CTD1) of the S1 subunit of the viral S protein. The relative MMGBSA binding energies show that silodosin has the best binding to the target. The constant velocity steered molecular dynamics (SMD) simulations show that silodosin preferentially interacts with the RBD S1 and has potential to act as an interfering compound between viral spike–host ACE2 interactions. Communicated by Ramaswamy H. Sarma
Collapse
Affiliation(s)
- Ibrahim E Awad
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Canada
| | | | - Sweta Sharma
- Department of Chemistry, University Institute of Engineering and Technology, Chhatrapati Shahu Ji Maharaj University, Kanpur, India
| | - Arpita Yadav
- Department of Chemistry, University Institute of Engineering and Technology, Chhatrapati Shahu Ji Maharaj University, Kanpur, India
| | - Raymond A Poirier
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Canada
| |
Collapse
|
10
|
Abu-saleh AAA, Awad I, Yadav A, Poirier RA. Computational Design of Potent Inhibitors for SARS-CoV-2’s Main Protease.. [DOI: 10.26434/chemrxiv.12548003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
In silico drug design can play a vital role in identifying promising drug candidates against COVID-19. Herein, we focused on the main protease of SARS-CoV-2 that plays crucial biological functions in the virus. We performed a ligand-based virtual screening followed by a docking screening for testing approved drugs and bioactive compounds listed in the DrugBank and ChEMBL databases. The top 8 docking results were advanced to all-atom MD simulations to study the relative stability of the protein-ligand interactions.Our results suggest several promising approved and bioactive inhibitors of SARS-CoV-2 Mpro.
Collapse
|
11
|
Abu-saleh AAA, Awad I, Yadav A, Poirier RA. Computational Design of Potent Inhibitors for SARS-CoV-2’s Main Protease.. [DOI: 10.26434/chemrxiv.12548003.v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
In silico drug design can play a vital role in identifying promising drug candidates against COVID-19. Herein, we focused on the main protease of SARS-CoV-2 that plays crucial biological functions in the virus. We performed a ligand-based virtual screening followed by a docking screening for testing approved drugs and bioactive compounds listed in the DrugBank and ChEMBL databases. The top 8 docking results were advanced to all-atom MD simulations to study the relative stability of the protein-ligand interactions.Our results suggest several promising approved and bioactive inhibitors of SARS-CoV-2 Mpro.
Collapse
Affiliation(s)
| | | | - Arpita Yadav
- University Institute of Engineering and Technology, CSJM University Kanpur India
| | | |
Collapse
|
12
|
Abu-Saleh AAAA, Sharma S, Yadav A, Poirier RA. Role of Asp190 in the Phosphorylation of the Antibiotic Kanamycin Catalyzed by the Aminoglycoside Phosphotransferase Enzyme: A Combined QM:QM and MD Study. J Phys Chem B 2020; 124:3494-3504. [DOI: 10.1021/acs.jpcb.0c01604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Abd Al-Aziz A. Abu-Saleh
- Chemistry Department, Memorial University, St. John’s, Newfoundland and Labrador A1B 3X7, Canada
| | - Sweta Sharma
- Department of Chemistry, University Institute of Engineering & Technology, Chhatrapati Shahu Ji Maharaj University, Kanpur 208024, India
| | - Arpita Yadav
- Department of Chemistry, University Institute of Engineering & Technology, Chhatrapati Shahu Ji Maharaj University, Kanpur 208024, India
| | - Raymond A. Poirier
- Chemistry Department, Memorial University, St. John’s, Newfoundland and Labrador A1B 3X7, Canada
| |
Collapse
|
13
|
|
14
|
|
15
|
Almatarneh MH, Barhoumi L, Al-Tayyem B, Abu-Saleh AAAA, AL-A’qarbeh MM, Abuorabi F, AlShamaileh E, Altarawneh M, Marashdeh A. Computational study for the second-stage cracking of the pyrolysis of ethylamine: Decomposition of methanimine, ethenamine, and ethanimine. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2015.10.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|