**Acknowledgement**

We have resumed the available structural information related to the retroviral integrase. We used this data to generate biologically relevant HIV-1 targets ‒ the unbound IN, the viral DNA (vDNA) and the IN•vDNA complex ‒ which represent with a certain level of reliabili‐

We have characterised the RAL binding, a very flexible molecule displaying the E/Z isomer‐ ism, to the active site of its HIV-1 targets which mimic the integrase states before and after the 3'-processing. The docked conformations represent a spectrum of possible conformation‐ al/configurational states. The best docking scores and poses confirm that the generated mod‐ el representing the IN•vDNA complex is the biologically relevant target of RAL, the strand transfer inhibitor. This finding is consistent with well-documented and commonly accepted inhibition mechanism of RAL, based on integral biological, biochemical and structural data.

RAL docking onto the IN•vDNA complex systematically generated the RAL chelated to Mg2+cations at the active site by the pharmacophore oxygen atoms. The identification of IN residues specifically interacting with RAL is likely a very difficult task and the exact modes of binding of this inhibitor remain a matter of debate. Most probably the flexible nature of RAL results in different conformations and the mode of binding may differ in terms of the interacting residues of the target, which trigger the alternative resistance phenomenon.

The identified RAL binding to the processed viral DNA shed light on a putative, even plau‐

We have implemented dynamic properties to the HIV-1 targets characterisation, particular‐ ly, the internal protein collective motions and the global conformational transition. Such transitions play an essential role in the function of many proteins, but experiments do not provide the atomic details on the path followed in going from one end structure to the other. For the dimeric IN, the transition pathway between the unbound and bound to vDNA is not known, which limits information of the cooperative mechanism in this typical allosteric sys‐ tem, where both tertiary and quaternary changes are involved. Description of the IN inter‐ mediate conformations open a way to localise the allosteric pockets, which in turn can be selected as the putative binding sites for small molecules in a virtual screening protocol.

Novel drugs, targeted the HIV-1 Integrase, outcome mainly due to the rapid emergence of RAL analogues (for example, GS-9137 or elvitegravir, MK-2048 and S/GSK 1349572, current‐ ly under clinical trials [93]). The clinical trials of several RAL analogues (BMS-707035, GSK-364735) were suspended. All these molecules specifically suppress the IN ST reaction. We conceive that the future HIV-1 integrase drug development will be mainly oriented to design of inhibitors with a mechanism of action that differs from that of RAL and its ana‐ logues. Distinct conceptions are potentially conceivable: (i) Design of the allosteric inhibi‐ tors, able to recognize specifically the binding sites that differ from the IN active site. Inhibitor V-165, belonging to such type inhibitors, prevents IN binding with the viral DNA such blocking 3'-processing reaction [94]. (ii) Design of the protein-protein inhibitors (PPIs) acting on interaction interface between either viral components (the IN monomers upon multimerization process or sub-units of the IN•vDNA complex) [95,96], or between viral

sible, step of the RAL inhibition mechanism.

Applications

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ty, two different enzymatic states of the HIV-1 over the retroviral integration process.

An Integrated View of the Molecular Recognition and Toxinology - From Analytical Procedures to Biomedical

The authors thank Dr. E. Laine for valuable discussions and for editorial assistance, I. Chau‐ vot de Beauchêne and S. Abdel-Azeim for providing of illustrative materials. This work is funded by the Centre National de la Recherche Scientifique (CNRS), Ecole Normale Supér‐ ieure (ENS) de Cachan and SIDACTION.
