Remdesivir: Mechanism of Metabolic Conversion from Prodrug to Drug

2021 ◽  
Vol 23 ◽  
Author(s):  
Saumya Kapoor ◽  
Gurudutt Dubey ◽  
Samima Khatun ◽  
Prasad V. Bharatam

Background: Remdesivir (GS-5734) has emerged as a promising drug during the challenging times of COVID-19 pandemic. Being a prodrug, it undergoes several metabolic reactions before converting to its active triphosphate metabolite. It is important to establish the atomic level details and explore the energy profile of the prodrug to drug conversion process. Methods: In this work, Density Functional Theory (DFT) calculations were performed to explore the entire metabolic path. Further, the potential energy surface (PES) diagram for the conversion of prodrug remdesivir to its active metabolite was established. The role of catalytic triad of Hint1 phosphoramidase enzyme in P-N bond hydrolysis was also studied on a model system using combined molecular docking and quantum mechanics approach. Results: The overall energy of reaction is 11.47 kcal/mol exergonic and the reaction proceeds through many steps requiring high activation energies. In the absence of a catalyst, the P-N bond breaking step requires 41.78 kcal/mol, which is reduced to 14.26 kcal/mol in a catalytic environment. Conclusion: The metabolic pathways of model system of remdesivir (MSR) were completely explored completely and potential energy surface diagrams at two levels of theory, B3LYP/6-311++G(d, p) and B3LYP/6-31+G(d), were established and compared. The results highlight the importance of an additional water molecule in the metabolic reaction. The P-N bond cleavage step of the metabolic process requires the presence of an enzymatic environment.

2007 ◽  
Vol 06 (03) ◽  
pp. 549-562
Author(s):  
ABRAHAM F. JALBOUT

The transition states for the H 2 NO decomposition and rearrangements mechanisms have been explored by the CBS-Q method or by density functional theory. Six transition states were located on the potential energy surface, which were explored with the Quadratic Complete Basis Set (CBS-Q) and Becke's one-parameter density functional hybrid methods. Interesting deviations between the CBS-Q results and the B1LYP density functional theory lead us to believe that further study into this system is necessary. In the efforts to further assess the stabilities of the transition states, bond order calculations were performed to measure the strength of the bonds in the transition state.


2017 ◽  
Vol 70 (4) ◽  
pp. 362 ◽  
Author(s):  
Young J. Hong ◽  
Dean J. Tantillo

An energetically viable (on the basis of results from density functional theory computations) pathway to the diterpene variediene is described. Only one of the three secondary carbocations along this pathway is predicted to be a minimum on the potential energy surface.


2017 ◽  
Vol 59 (2) ◽  
Author(s):  
Jamshid Najafpour

<p>We have calculated the intermolecular potential energy surface (IPES) of the dimer of cubic N8 cluster using <em>ab initio </em>and the density functional theory (DFT) calculations. The <em>ab initio </em>(HF/3- 21G(d)) and DFT (B3LYP/6-31G(d) and aug-cc-pVDZ) calculations were performed for two relative orientations of N8-N8 system as a function of separation distance between the centers of cubic N8 clusters. In this research, the IPES, <em>U</em>(<em>r</em>), of the N8-N8 system is studied, where the edge of N8 approaches to face or edge of the other considered N8. Then, the Lennard-Jones (12-6) and (22-11) adjustable parameters are fitted to the computed interaction energies for edge-face and edge-edge orientations. In this research for the first time, the IPESs proportionated to the Lennard-Jones (22-11) potential are derived that are compatible with the computed IPES curves. Assuming a set of Lennard-Jones parameters, the second virial coefficients are obtained for the N8-N8 complex at a temperature range of 298 to 1000 K. Both the corrected and uncorrected basis set superposition error (BSSE) results are presented confirming the significance of including BSSE corrections.</p>


Author(s):  
Anouar el Guerdaoui ◽  
Yassine el Kahoui ◽  
Malika Bourjila ◽  
Rachida Tijar ◽  
Abderrahman el Gridani

We performed here a systematic ab initio calculations on neutral gas-phase L-proline. A total of 8 local minima were located by geometry optimization of the trial structures using density functional theory (DFT) with B3LYP three parameter hybrid potential coupled with the 6-31G)d( basis set. The absolute minimum obtained will be subject to a rigid potential energy surface (PES) scan by rotating its carboxylic group using the same method with more accurate basis set B3LYP/6-311++G(d,p), to get a deeper idea about its conformational stability. The main aim of the present work was the study of the rigidity of the L-proline structure and the puckering of its pyrrolidine ring.


2020 ◽  
Author(s):  
Zoi Salta ◽  
Marc E. Segovia ◽  
Aline Katz ◽  
Nicola Tasinato ◽  
Vincenzo Barone ◽  
...  

Thione S-methylide (TSM), the parent species of the thiocarbonyl ylide family, is a 1,3-dipolar, planar species on the [C2SH4] potential energy surface (PES), which has not shared the richness of studies dedicated to its isomers, the cyclic thiirane (THI), and the keto-enol pair vinyl thiol (VTH)/thioacetaldehyde (THA). While the conrotatory ring closure reaction toward THI was studied in the ‘90s, no complete analysis of the PES is available in the literature. In the present paper, we report a computational study of the reaction scheme linking all species on that PES. We employ several levels of calculation, ranging from density functional theory (DFT), through CCSD(T) based composite schemes, to CASSCF/CASPT2 multi-reference procedures, to find the best description of TSM, its isomers, and the transition states (TSs) ruling their interconversion. Fragmentation of TSM, THA and THI were investigated and compared to the available experimental information. We found that the B2PLYP-D3 functional, contrary to M06-2XD3 or B97X-D, describes well the geometry of both TSM and the transition state connecting it to THI. The reverse barrier, from THI to TSM, amounts to 52.2 kcal mol-1 (to be compared to 17.6 kcal mol-1 for the direct one), thus explaining why, in general, thiocarbonyl ylides cannot be prepared from thiiranes. Conversion of THI to VTH implies also a large barrier, explaining why the reaction has been observed only at high temperatures. The fragmentation of THI to S(3P) or S(1D) and ethylene was also explored, together with the decomposition to H2S plus acetylene. Open species, both in triplet and singlet states, were identified as intermediates in the fragmentations, and their energies were found to be lower than the transition state for the isomerization of THI to VTH, thus explaining the preference for fragmentation over isomerization at relatively low temperatures.


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