Topical Perspectives
Design and computational support for the binding stability of a new CCR5/CXCR4 dual tropic inhibitor: Computational design of a CCR5/CXCR4 drug

https://doi.org/10.1016/j.jmgm.2017.02.012Get rights and content

Highlights

  • Binding motifs of a previously proposed CCR5/CXCR4 dual tropic inhibitor are studied.

  • π-stacking and electrostatics drive binding between ligand and receptor residues.

  • Unfavorable desolvation of active site Glu and Asp residues offsets favorable motifs.

  • The replacement of the γ-carbon of the ligand piperidine ring deters such an offset.

Abstract

The human immunodeficiency virus (HIV) infects healthy human cells by binding to the glycoprotein cluster of differentiation 4 receptors on the surface of helper T-cells, along with either of two chemokine receptors, Csingle bondC chemokine receptor type 5 (CCR5) or C-X-C chemokine receptor type 4 (CXCR4). Recently, a pyrazolo-piperdine ligand was synthesized and the corresponding biological data showed good binding to both chemokine receptors, effectively blocking HIV-1 entry. Here, we exhaustively assess the atomistic binding interactions of this compound with both CCR5 and CXCR4, and we find that binding is driven by π-stacking interactions between aromatic rings on the ligand and receptor residues, as well as electrostatic interactions involving the protonated piperidine nitrogen. However, these favorable binding interactions were partially offset by unfavorable desolvation of active site glutamates and aspartates, prompting our proposal of a new, synthetically-accessible derivative designed to increase the electrostatic interactions without compromising the π-stacking features.

Introduction

Over 35 million people worldwide live with the human immunodeficiency virus (HIV), a lentivirus that ultimately leads to the onset of acquired immunodeficiency syndrome (AIDS). Recently, a dual-tropic inhibitor has been reported that could prevent HIV-1 from attacking healthy T-cells [1]. The earliest known receptor to play a role in the HIV infection of healthy cells was the glycoprotein cluster of differentiation 4 (CD4) on the surface of helper T-cells. Designing drugs to inhibit CD4 receptors is a difficult task because helper T-cells are a vital part of the human immune defense. Through various experiments [2], [3], [4], [5], CD4 helper T-cells have been shown to prevent immune system failures as well as autoimmune system diseases. HIV targets the CD4 receptor to gain entry into human T-cells. Several early studies [6], [7], [8], [9] showed the selective reduction of CD4 helper T-cells by HIV. For instance, Gottlieb et al. [6] used monoclonal antibody analysis to show that HIV-afflicted individuals displayed a major decrease in T-helper cells along with a concomitant increase in T-suppressor cells. Klatzmann et al. [7] found that antibody inhibition of CD4 receptors prevented HIV infection of the cell. Another experimental study in 1993 [5] utilized PCR to confirm the dependency on CD4 receptors for HIV1 infection of healthy human cells. However, it was also found that HIV inhibition of helper T-cells was not solely CD4-dependent, but was codependent on CD4 and chemokine receptors [10]. Two chemokine receptors, Csingle bondC chemokine receptor type 5 (CCR5) and C-X-C chemokine receptor type 4 (CXCR4), were determined to be necessary for the full infection of human helper T-cells by HIV. Experimentally it has been shown, in the presence of HIV-1, that co-expression of CD4 with CCR5 or CXCR4 correlated with an increase in helper T-cells, suggesting a codependence on CD4 and the chemokine receptors [11], [12].

Chemokines are generally responsible for pro-inflammatory behaviors of leukocyte cells. CCR5 is a β-chemokine that tends to exist on monocytes, lymphocytes, basophils, and eosinophils, while CXCR4 is an α-chemokine that is primarily found on neutrophils [13], [14]. Furthermore, it has been found that the expression of CCR5 and CXCR4 receptors is not uniform and can show large variance between T-cell lines and subsets [15]. It is for this reason that HIV treatment methods have required a medley of drugs, specific to the level of expression of each HIV target receptor in an infected individual.

The discovery of CD4/CCR5 and CD4/CXCR4 codependence of HIV inhibition opened new pathways for therapeutic targets [10], [11], [12]. To date, the most successful form of treatment for HIV and AIDS is highly active antiretroviral therapy (HAART), which utilizes a combination of several drugs to ultimately slow the advancement to AIDS through various inhibition of nucleoside/non-nucleoside reverse transcriptase, entry and fusion, integrase, and protease [16]. The utilization of several single-target inhibitors can lead to unintended side effects caused by drug–drug interactions, prompting the need for a single inhibitor capable of multi-site inhibition [1], [17], [18], [19].

HIV infects healthy human helper T-cells by binding to CCR5 and/or CXCR4, thereby prompting the development of dual CCR5/CXCR4 inhibitors [1], [20], [21]. Most recently, one of the more effective CCR5 and CXCR4 dual-inhibitor drugs was reported by Liotta and coworkers [1]. Compound 3 (Fig. 1) was shown to be an effective drug with IC50 values of 36 μM (CCR5) and 52 μM (CXCR4); however, the mechanism for binding was not known.

In this study, we aimed to 1) evaluate the binding dynamics between 3 and CCR5 and CXCR4, 2) determine the atomistic interactions of 3 with each receptor, and 3) design a new, synthetically-accessible derivative of 3 that would increase the inhibition of CCR5 and CXCR4. We believe that a better understanding of the atomistic details and molecular dynamics of these protein-ligand complexes will provide fundamental information with which to better assess potential drugs for dual chemokine receptor ligation.

Section snippets

Structure retrieval

Structures of the CCR5 chemokine receptor, and the CXCR4 chemokine receptor in complex with Compound 3, were obtained through personal communications with Dr. Dennis Liotta at Emory University. The initial docking of these complexes has been described previously [1]. The CCR5 receptor was taken from PDB 4MBS [22]. Two CXCR4 crystal structures were published in 2010, one inhibited by IT1t (PDB ID: 3ODU) and the other by CVX15 (PDB ID: 3OE0) [23]. The sequences in these two structures are very

Results and discussion

The purpose of this study was to obtain an atomistic understanding of the binding of a previously reported dual-inhibitor with the CCR5 and CXCR4 HIV receptors [1]. Using this information, we designed and computationally tested a synthetically accessible derivative of the original compound, that shows enhanced binding to these receptors. Our ability to compute binding free energies for the original Compound 3, in agreement with previously published experimental results, support the viability of

Conclusion

An atomistic understanding of the inhibition of CCR5 and CXCR4 by the Liotta et al. synthesized 3 has been determined. Based on both experimental and computational results, 3 shows higher affinity for CCR5 than CXCR4. 3 remained within the active site for all 30 molecular dynamics simulations, and the trajectories from those simulations produced MM-GBSA binding energies in good agreement with experiment. The binding of 3 could be attributed to two main factors: three aromatic rings capable of

Author contributions

C.A.P. conceived the study. All authors designed the computational approaches. C.A.T performed the computational work. C.A.T wrote the manuscript. C.A.P. C.A.T., and B.R.M. edited the manuscript.

Acknowledgements

C.T. acknowledges support from the UR Undergraduate Research Program. This work was also supported by awards from the National Science Foundation (CHE-0809462, CHE-0958696, MCB-1049954 and CHE-1213271). C.P. also acknowledges support from the Camille and Henry Dreyfus Foundation through receipt of a Henry Dreyfus Teacher – Scholar award. All calculations were carried out at the University of Richmond. Computational resources were provided, in part, by the MERCURY supercomputer consortium under

References (45)

  • M.H. Collin et al.

    Res. Virol.

    (1993)
  • J.S. McDougal et al.

    J. Immunol. Methods

    (1985)
  • P.J. Maddon et al.

    Cell

    (1986)
  • H. Choe et al.

    Cell

    (1996)
  • M. Baggiolini et al.

    Adv. Immunol.

    (1993)
  • T.J. Schall et al.

    Curr. Opin. Immunol.

    (1994)
  • E. Jenwitheesuk et al.

    Trends Pharmacol. Sci.

    (2008)
  • M.P.F.R.A. Jacobson et al.

    J. Mol. Biol.

    (2002)
  • W. Humphrey et al.

    J. Mol. Graph.

    (1996)
  • J.P. Ryckaert et al.

    J. Comput. Phys.

    (1977)
  • B.D. Cox et al.

    ACS Med. Chem. Lett.

    (2015)
  • M.A. Linterman et al.

    J. Exp. Med.

    (2009)
  • C. King et al.

    Annu. Rev. Immunol.

    (2008)
  • N. Simpson et al.

    Arthritis Rheum.

    (2010)
  • M.S. Gottlieb et al.

    New Engl. J. Med.

    (1981)
  • D. Klatzmann et al.

    Nature

    (1984)
  • A.G. Dalgleish et al.

    Nature

    (1984)
  • O. Delezay et al.

    AIDS

    (1997)
  • B. Lee et al.

    Proc. Natl. Acad. Sci.

    (1999)
  • R. Detels et al.

    JAMA

    (1998)
  • A. Herschhorn et al.

    Nat. Chem. Biol.

    (2014)
  • K. Watson Buckheit et al.

    Antimicrob. Agents Chemother.

    (2011)
  • Cited by (5)

    • Discovery of HIV entry inhibitors via a hybrid CXCR4 and CCR5 receptor pharmacophore‐based virtual screening approach

      2020, European Journal of Pharmaceutical Sciences
      Citation Excerpt :

      Compound 6 showed a fairly negative energy value for glutamate interaction due to the presence of two protonated nitrogen atoms of the piperazine ring, which counteracted the desolvation effect. This more negative per-residue decomposition value of Glu288 in CXCR4 is supported by the evidence from Taylor et al. (2017). They changed the protonated piperidine ring (Cox et al., 2015) to a doubly protonated piperazine ring aiming at increasing the electrostatic interactions, hence counteracting the desolvation effect.

    View full text