The present art of drug discovery and design of new drugs is based on suicidal irreversible inhibitors. Covalent inhibition is the strategy that is used to achieve irreversible inhibition. Irreversible inhibitors interact with their targets in a time-dependent fashion, and the reaction proceeds to completion rather than to equilibrium. Covalent inhibitors possessed some significant advantages over non-covalent inhibitors such as covalent warheads can target rare, non-conserved residue of a particular target protein and thus led to development of highly selective inhibitors, covalent inhibitors can be effective in targeting proteins with shallow binding cleavage which will led to development of novel inhibitors with increased potency than non-covalent inhibitors. Several computational approaches have been developed to simulate covalent interactions; however, this is still a challenging area to explore. Covalent molecular docking has been recently implemented in the computer-aided drug design workflows to describe covalent interactions between inhibitors and biological targets. In this review we highlight: (i) covalent interactions in biomolecular systems; (ii) the mathematical framework of covalent molecular docking; (iii) implementation of covalent docking protocol in drug design workflows; (iv) applications covalent docking: case studies and (v) shortcomings and future perspectives of covalent docking. To the best of our knowledge; this review is the first account that highlights different aspects of covalent docking with its merits and pitfalls. We believe that the method and applications highlighted in this study will help future efforts towards the design of irreversible inhibitors.

Herein, for the first time, we report the flap opening and closing in Plasmepsin proteases - plasmepsin II (PlmII) was used as a prototype model. We proposed different combined parameters to define the asymmetric flap motion; the distance, d1, between the flap tip residues (Val78 and Leu292); the dihedral angle, ϕ; in addition to TriCα angles Val78-Asp34-Leu292, θ1, and Val78-Asp214-Leu292, θ2. Only three combined parameters, the distance, d1, the dihedral angle, ϕ, and the TriCα angle, θ1, were found to appropriately define the observed "twisting' motion during the flap opening and closing. The coordinated motions of the proline-rich loop adjacent to the binding cavity rim appeared to exert steric hindrance on the flap residues, driving the flap away from the active site cavity. This loop may also have increased movements around the catalytic dyad residue, Asp214, making TriCα, θ2, unreliable in describing the flap motion. The full flap opening at d1, 23.6 Å, corresponded to the largest TriCα angle, θ1, at 78.6° on a ∼46 ns time scale. Overall the average θ1 and θ2 for the bound was ∼46° and ∼53°, respectively, compared to ∼50° and ∼59° for the Apo PlmII, indicating a drastic increase in TriCα as the active site cavity opens. Similar trends in the distance, d1, and the dihedral angle, ϕ, were observed during the simulation. The asymmetrical opening of the binding cavity was best described by the large shift in ϕ from -33.91° to +21.00° corresponding to the partial opening of the flap in the range of 22-31 ns. Though, the dihedral angle described the twisting of the flap, the extent of flap opening can appropriately be defined by combining d1 and θ1. The results presented here, on the combined parameters, will certainly augment current efforts in designing potent structure-based inhibitors against plasmepsins.

The emergence of different drug resistant strains of HIV-1 reverse transcriptase (HIV RT) remains of prime interest in relation to viral pathogenesis as well as drug development. Amongst those mutations, M184V was found to cause a complete loss of ligand fitness. In this study, we report the first account of the molecular impact of M184V mutation on HIV RT resistance to 3TC (lamivudine) using an integrated computational approach. This involved molecular dynamics simulation, binding free energy analysis, principle component analysis (PCA) and residue interaction networks (RINs). Results clearly confirmed that M184V mutation leads to steric conflict between 3TC and the beta branched side chain of valine, decreases the ligand (3TC) binding affinity by ∼7 kcal mol(-1) when compared to the wild type, changes the overall conformational landscape of the protein and distorts the native enzyme residue-residue interaction network. The comprehensive molecular insight gained from this study should be of great importance in understanding drug resistance against HIV RT as well as assisting in the design of novel reverse transcriptase inhibitors with high ligand efficacy on resistant strains.