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**Chapter 15**

**The HIV-1 Integrase: Modeling and Beyond**

Molecular recognition is a fundamental phenomenon observed in all biological systems organisation ‒ proteins, nucleic acids and their complexes, cells and tissues. Molecular recognition is governed by specific attractive interactions between two or more partner molecules through non-covalent bonding such as hydrogen bonds, metal coordination, electrostatic effects, hydrophobic and van der Waals interactions. The partners – recep‐ tor(s) and substrate(s) or ligands ‒ involved in molecular recognition, exhibit molecular complementarity that can be adjusted over the recognition process. Competition and co‐ operation, the two opposite natural effects contributing to selective and specific recogni‐ tion between participating partners, are the basic principles of substrate/ligand/inhibitor

The tertiary structures of biological objects (proteins and nucleic acids) are formed mainly by hydrogen bonds (enthalpic contributions) and by hydrophobic contacts (mostly entropic contributions). With a few exceptions, (e.g. ligand binding to the Ah receptor), the organisa‐

In the process of a ligand binding to its target the hydrogen bonds contribute to (i) the orien‐ tation of the substrates/ligands/inhibitors by a receptor, frequently associated with a confor‐ mational/structural adjustment of the interacting agents; (ii) the specific recognition of substrates/ligands/inhibitors and selectivity between sterically or structurally similar but bi‐ ochemically different species; (iii) the affinity of ligands/inhibitors ‒ the most decisive factor

To describe the pharmacological properties of a given ligand or inhibitor, the knowledge of the site where the inhibitor is to bind with the target and of which interaction(s) control the specific recognition of the inhibitor by its target(s), represents a corner stone factor. Only a limited number of target-ligand molecular complexes have been characterized experimen‐

> © 2013 Arora and Tchertanov; licensee InTech. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

© 2013 Arora and Tchertanov; licensee InTech. This is a paper distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use,

distribution, and reproduction in any medium, provided the original work is properly cited.

tion of ligand-protein complexes depends primarily on hydrogen bonding.

Rohit Arora and Luba Tchertanov

http://dx.doi.org/10.5772/52344

or protein binding to its targets.

**1. Introduction**

in drug design.

Additional information is available at the end of the chapter
