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Structural Chemistry

, Volume 30, Issue 1, pp 409–417 | Cite as

Unraveling the concerted catalytic mechanism of the human immunodeficiency virus type 1 (HIV-1) protease: a hybrid QM/MM study

  • Monsurat M. Lawal
  • Zainab K. Sanusi
  • Thavendran Govender
  • Gideon F. Tolufashe
  • Glenn E. M. Maguire
  • Bahareh Honarparvar
  • Hendrik G. KrugerEmail author
Original Research
  • 88 Downloads

Abstract

We give an account of a one-step concerted catalytic mechanism of HIV-1 protease (PR) hydrolysis of its natural substrate using a hybrid QM/MM method. The mechanism is a general acid–base model having both catalytic aspartate groups participating and a water molecule attacking the natural substrate synchronously. Three different pathways were investigated: a concerted acyclic transition state (TS) mechanistic route, a concerted 6-membered cyclic TS process involving one water molecule, and another 6-membered ring TS pathway involving two water molecules. Activation free energies of approximately 15.2 and 16.6 kcal mol−1 were obtained for both concerted acyclic and the other possible reaction pathway involving two water molecules in the active site, respectively. The activation free energies are comparable to experimentally derived data of 15.69 kcal mol−1. The outcome of the present work provides a plausible theoretical benchmark for the concerted enzymatic mechanism of HIV-1 PR and can be applied to related enzymatic processes.

Keywords

HIV-1 protease Natural substrate QM/MM (Our own N-layered Integrated molecular Orbital and molecular Mechanics ONIOM) method Concerted transition states Catalytic mechanism 

Notes

Acknowledgements

We are grateful to the Centre for High Performance Computing (www.chpc.ac.za) for computational resources.

Funding information

The authors thank the College of Health Sciences, University of KwaZulu-Natal, Asphen Pharmacare, Medical Research Council, and the National Research Foundation (all in South Africa) for the financial support.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Supplementary material

11224_2018_1251_MOESM1_ESM.docx (3.1 mb)
ESM 1 (DOCX 3145 kb)

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Authors and Affiliations

  1. 1.Catalysis and Peptide Research Unit, School of Health SciencesUniversity of KwaZulu-NatalDurbanSouth Africa
  2. 2.School of Chemistry and PhysicsUniversity of KwaZulu-NatalDurbanSouth Africa

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