The role of weak interactions in evaluation of inhibitory potential of Indinavir as an HIV protease inhibitor and its comparison with innovative drug candidates
Designing and employing enzyme inhibitors against viral enzymes is one of the innovative and efficient approaches to treating viral diseases. These inhibitors can disrupt the viral replication cycle by deactivating vital enzymes, thereby curbing the spread of viral infections by reducing their popul...
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| Vydané v: | Computers in biology and medicine Ročník 187; s. 109675 |
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| Hlavní autori: | , |
| Médium: | Journal Article |
| Jazyk: | English |
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United States
Elsevier Ltd
01.03.2025
Elsevier Limited |
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| ISSN: | 0010-4825, 1879-0534, 1879-0534 |
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| Abstract | Designing and employing enzyme inhibitors against viral enzymes is one of the innovative and efficient approaches to treating viral diseases. These inhibitors can disrupt the viral replication cycle by deactivating vital enzymes, thereby curbing the spread of viral infections by reducing their population. So far, inhibitors have been designed, validated, and introduced for these enzymes. In this study, we designed the drug Indinavir and 20 analogs using Hartree-Fock and DFT methods to enhance the design of more potent protease enzyme inhibitors. Frequency calculations were performed at similar computational levels for all examined drugs and their designed analogs, revealing no negative frequencies. The Pharmacokinetics of the inhibitors were assessed, and inhibitors were screened, with those exhibiting minimal toxicity introduced as drug candidates for further evaluation. The best binding mode of Indinavir and the designed drugs at the protein binding site were determined using molecular docking studies. For the IND20 inhibitor with the best binding mode, an energy of −13.03 (kcal/mol) was reported. Finally, molecular dynamics simulations were conducted to evaluate the inhibitory mechanism of the recommended inhibitor on the protease enzyme. The relevant analyses during the simulation period showed that the designed drug IND20 exhibited better performance in inhibiting the HIV-1 protease enzyme compared to Indinavir.
[Display omitted]
•The role of weak interactions such as hydrogen bonding in inhibitory ability have been investigated completely.•The study focuses on the design and validation of protease enzyme inhibitors, highlighting Indinavir and its analogs.•Pharmacokinetics was assessed, and minimally toxic inhibitors were selected as candidates for further drug development. |
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| AbstractList | Designing and employing enzyme inhibitors against viral enzymes is one of the innovative and efficient approaches to treating viral diseases. These inhibitors can disrupt the viral replication cycle by deactivating vital enzymes, thereby curbing the spread of viral infections by reducing their population. So far, inhibitors have been designed, validated, and introduced for these enzymes. In this study, we designed the drug Indinavir and 20 analogs using Hartree-Fock and DFT methods to enhance the design of more potent protease enzyme inhibitors. Frequency calculations were performed at similar computational levels for all examined drugs and their designed analogs, revealing no negative frequencies. The Pharmacokinetics of the inhibitors were assessed, and inhibitors were screened, with those exhibiting minimal toxicity introduced as drug candidates for further evaluation. The best binding mode of Indinavir and the designed drugs at the protein binding site were determined using molecular docking studies. For the IND20 inhibitor with the best binding mode, an energy of −13.03 (kcal/mol) was reported. Finally, molecular dynamics simulations were conducted to evaluate the inhibitory mechanism of the recommended inhibitor on the protease enzyme. The relevant analyses during the simulation period showed that the designed drug IND20 exhibited better performance in inhibiting the HIV-1 protease enzyme compared to Indinavir. Designing and employing enzyme inhibitors against viral enzymes is one of the innovative and efficient approaches to treating viral diseases. These inhibitors can disrupt the viral replication cycle by deactivating vital enzymes, thereby curbing the spread of viral infections by reducing their population. So far, inhibitors have been designed, validated, and introduced for these enzymes. In this study, we designed the drug Indinavir and 20 analogs using Hartree-Fock and DFT methods to enhance the design of more potent protease enzyme inhibitors. Frequency calculations were performed at similar computational levels for all examined drugs and their designed analogs, revealing no negative frequencies. The Pharmacokinetics of the inhibitors were assessed, and inhibitors were screened, with those exhibiting minimal toxicity introduced as drug candidates for further evaluation. The best binding mode of Indinavir and the designed drugs at the protein binding site were determined using molecular docking studies. For the IND20 inhibitor with the best binding mode, an energy of -13.03 (kcal/mol) was reported. Finally, molecular dynamics simulations were conducted to evaluate the inhibitory mechanism of the recommended inhibitor on the protease enzyme. The relevant analyses during the simulation period showed that the designed drug IND20 exhibited better performance in inhibiting the HIV-1 protease enzyme compared to Indinavir.Designing and employing enzyme inhibitors against viral enzymes is one of the innovative and efficient approaches to treating viral diseases. These inhibitors can disrupt the viral replication cycle by deactivating vital enzymes, thereby curbing the spread of viral infections by reducing their population. So far, inhibitors have been designed, validated, and introduced for these enzymes. In this study, we designed the drug Indinavir and 20 analogs using Hartree-Fock and DFT methods to enhance the design of more potent protease enzyme inhibitors. Frequency calculations were performed at similar computational levels for all examined drugs and their designed analogs, revealing no negative frequencies. The Pharmacokinetics of the inhibitors were assessed, and inhibitors were screened, with those exhibiting minimal toxicity introduced as drug candidates for further evaluation. The best binding mode of Indinavir and the designed drugs at the protein binding site were determined using molecular docking studies. For the IND20 inhibitor with the best binding mode, an energy of -13.03 (kcal/mol) was reported. Finally, molecular dynamics simulations were conducted to evaluate the inhibitory mechanism of the recommended inhibitor on the protease enzyme. The relevant analyses during the simulation period showed that the designed drug IND20 exhibited better performance in inhibiting the HIV-1 protease enzyme compared to Indinavir. Designing and employing enzyme inhibitors against viral enzymes is one of the innovative and efficient approaches to treating viral diseases. These inhibitors can disrupt the viral replication cycle by deactivating vital enzymes, thereby curbing the spread of viral infections by reducing their population. So far, inhibitors have been designed, validated, and introduced for these enzymes. In this study, we designed the drug Indinavir and 20 analogs using Hartree-Fock and DFT methods to enhance the design of more potent protease enzyme inhibitors. Frequency calculations were performed at similar computational levels for all examined drugs and their designed analogs, revealing no negative frequencies. The Pharmacokinetics of the inhibitors were assessed, and inhibitors were screened, with those exhibiting minimal toxicity introduced as drug candidates for further evaluation. The best binding mode of Indinavir and the designed drugs at the protein binding site were determined using molecular docking studies. For the IND20 inhibitor with the best binding mode, an energy of −13.03 (kcal/mol) was reported. Finally, molecular dynamics simulations were conducted to evaluate the inhibitory mechanism of the recommended inhibitor on the protease enzyme. The relevant analyses during the simulation period showed that the designed drug IND20 exhibited better performance in inhibiting the HIV-1 protease enzyme compared to Indinavir. [Display omitted] •The role of weak interactions such as hydrogen bonding in inhibitory ability have been investigated completely.•The study focuses on the design and validation of protease enzyme inhibitors, highlighting Indinavir and its analogs.•Pharmacokinetics was assessed, and minimally toxic inhibitors were selected as candidates for further drug development. Designing and employing enzyme inhibitors against viral enzymes is one of the innovative and efficient approaches to treating viral diseases. These inhibitors can disrupt the viral replication cycle by deactivating vital enzymes, thereby curbing the spread of viral infections by reducing their population. So far, inhibitors have been designed, validated, and introduced for these enzymes. In this study, we designed the drug Indinavir and 20 analogs using Hartree-Fock and DFT methods to enhance the design of more potent protease enzyme inhibitors. Frequency calculations were performed at similar computational levels for all examined drugs and their designed analogs, revealing no negative frequencies. The Pharmacokinetics of the inhibitors were assessed, and inhibitors were screened, with those exhibiting minimal toxicity introduced as drug candidates for further evaluation. The best binding mode of Indinavir and the designed drugs at the protein binding site were determined using molecular docking studies. For the IND20 inhibitor with the best binding mode, an energy of -13.03 (kcal/mol) was reported. Finally, molecular dynamics simulations were conducted to evaluate the inhibitory mechanism of the recommended inhibitor on the protease enzyme. The relevant analyses during the simulation period showed that the designed drug IND20 exhibited better performance in inhibiting the HIV-1 protease enzyme compared to Indinavir. AbstractDesigning and employing enzyme inhibitors against viral enzymes is one of the innovative and efficient approaches to treating viral diseases. These inhibitors can disrupt the viral replication cycle by deactivating vital enzymes, thereby curbing the spread of viral infections by reducing their population. So far, inhibitors have been designed, validated, and introduced for these enzymes. In this study, we designed the drug Indinavir and 20 analogs using Hartree-Fock and DFT methods to enhance the design of more potent protease enzyme inhibitors. Frequency calculations were performed at similar computational levels for all examined drugs and their designed analogs, revealing no negative frequencies. The Pharmacokinetics of the inhibitors were assessed, and inhibitors were screened, with those exhibiting minimal toxicity introduced as drug candidates for further evaluation. The best binding mode of Indinavir and the designed drugs at the protein binding site were determined using molecular docking studies. For the IND20 inhibitor with the best binding mode, an energy of −13.03 (kcal/mol) was reported. Finally, molecular dynamics simulations were conducted to evaluate the inhibitory mechanism of the recommended inhibitor on the protease enzyme. The relevant analyses during the simulation period showed that the designed drug IND20 exhibited better performance in inhibiting the HIV-1 protease enzyme compared to Indinavir. |
| ArticleNumber | 109675 |
| Author | Sabaghian, Hanieh Yoosefian, Mehdi |
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| Keywords | Drug design Acquired immunodeficiency syndrome (AIDS) Pharmacokinetics HIV protease enzyme Indinavir |
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| Title | The role of weak interactions in evaluation of inhibitory potential of Indinavir as an HIV protease inhibitor and its comparison with innovative drug candidates |
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