[HTML][HTML] Effect of biomolecular conformation on docking simulation: a case study on a potent HIV-1 protease inhibitor

N Razzaghi-Asl, S Sepehri, A Ebadi, R Miri… - Iranian journal of …, 2015 - ncbi.nlm.nih.gov
Human immunodeficiency virus infection/acquired immunodeficiency syndrome (HIV/AIDS)
is a disease pertained to the human immune system. Given its crucial role in viral replication …

[PDF][PDF] A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model

TM Salih - Iraqi Journal of Pharmaceutical Sciences (P-ISSN 1683 …, 2022 - iasj.net
Flexible molecular docking is a computational method of structure-based drug design. This
method is used to evaluate binding interactions between receptor and ligand and identify …

Studies on flexibility and binding affinity of Asp25 of HIV-1 protease mutants

R Purohit, R Rajasekaran, C Sudandiradoss… - International journal of …, 2008 - Elsevier
We have investigated and highlighted the behavior of binding residue, Asp25 by
computational analysis, which play an important role in understanding docking process with …

The role of weak interactions in evaluation of inhibitory potential of Indinavir as an HIV protease inhibitor and its comparison with innovative drug candidates

M Yoosefian, H Sabaghian - Computers in Biology and Medicine, 2025 - Elsevier
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 …

Analysis of CYP3A4-HIV-1 protease drugs interactions by computational methods for Highly Active Antiretroviral Therapy in HIV/AIDS

M Jayakanthan, S Chandrasekar… - Journal of Molecular …, 2010 - Elsevier
HIV infected patients often take at least three anti-HIV drugs together in Highly Active
Antiretroviral Therapy (HAART) and/or Ritonavir-Boosted Protease Inhibitor Therapy (PI/r) to …

Molecular dynamics and free energy studies on the wild-type and mutated HIV-1 protease complexed with four approved drugs: mechanism of binding and drug …

S Alcaro, A Artese… - Journal of chemical …, 2009 - ACS Publications
The current strategy to improve the quality of life of Human Immunodeficiency Virus (HIV)
infected individuals through suppressing viral replication and maintaining the virus at low to …

Decoding molecular mechanism underlying binding of drugs to HIV-1 protease with molecular dynamics simulations and MM-GBSA calculations

YX Yu, WT Liu, HY Li, W Wang, HB Sun… - SAR and QSAR in …, 2021 - Taylor & Francis
ABSTRACT HIV-1 protease (PR) is thought to be efficient targets of anti-AIDS drug design.
Molecular dynamics (MD) simulations and multiple post-processing analysis technologies …

Multiple molecular dynamics simulations and free-energy predictions uncover the susceptibility of variants of HIV-1 protease against inhibitors darunavir and KNI-1657

R Wang, Q Zheng - Langmuir, 2021 - ACS Publications
HIV-1 protease (PR) is considered to be the main targets of anti-AIDS drug design because
of its role in the proteolytic processing of viral polyproteins. However, the emergence of drug …

[PDF][PDF] Molecular docking studies and comparative binding mode analysis of FDA approved HIV protease inhibitors

PK Deb, A Junaid, D El-Rabie, TY Hon… - Asian Journal of …, 2014 - researchgate.net
The HIV protease enzyme (maturation enzyme) is one of the most promising therapeutic
targets for the treatment of AIDS. Due to the mutation in the virus, there is always room for …

Molecular dynamics and free energy studies on the wild-type and double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related inhibitors …

T Hou, R Yu - Journal of medicinal chemistry, 2007 - ACS Publications
The V82F/I84V double mutation is considered as the key residue mutation of the HIV-1
protease drug resistance because it can significantly lower the binding affinity of protease …