Madhur Mishra, Mohammed Haris Siddiqui
Department of Biotechnology, Microbiology and Bioinformatics, Integral University, Lucknow- 226026, India.

ABSTRACT

The HIV-1 protease enzyme is conscientious for the post translational processing of the viral Gag and Gag-Pol polyproteins to yield the structural proteins. The necessity of this enzyme (HIV-1 Protease) for the maturation of provirus and completion of virus life cycle makes it a promising target for Anti-Retroviral therapy. Fortunately for HIV virus and unfortunately for humans the viral reverse transcriptase enzyme lacks proofreading activity and has a very poor processivity. Due to lack of proofreading activity there is approximately 10 to 100 folds increase in probability of error by the enzyme because of which the virus quickly becomes resistant to drugs. In the work presented herein factors affecting drug stability have been predicted with the help of three proteins whose PDB ID’s are 1HPV (wild), 2B7Z (mutated), and 1TW7 (multidrug resistant or cross resistant). After structural analyses studies it was observed that the flap domain remains in its closed conformation in wild protease (1HPV) and subsequently it shifts towards its open conformation, resulting in the increase in the rate of mutation subsequently leading the flap tip to become more flexible and in semi open state. The results clearly indicate that the area of the active site binding pocket increases from 581.9Å to 996.5Å with the increase in the rate of mutation. It was further inferred upon that the mutation in some of active site residues (V82A, I84V) led to the random loss in the hydrophobicity which fell down from 1.732 to 0.356 inside the binding pocket of the active site. At last we arrived to the conclusion that greater is the active site binding pocket area, the more flexible is the semi open flap and the random loss in hydrophobic environment leads to the protease becoming resistant to all the available drugs. A derivative of Indinavir (IND1) has been designed and evaluated considering all factors affecting drug stability and on the basis of the results obtained it was found out that the newly designed derivative gives better insilco results to qualify as a drug lead than the available standard drug Indinavir against mutated protease.IND1 showed least minimum binding energy of -8.80 Kcal/mole, least Ki value of 0.35 μM, maximum number of hydrogen bonds(7), good ADME properties and less toxicity than Indinavir which are the prerequisites for a drug lead to be potent and effective. At the last we arrived to the conclusion that our study opens up the hidden potential of insilico tools to design new analogs for the efficient and effective treatment of harmful and infectious diseases.Read more…