Structure – based drug design is normally referred to as the designing of the drug based on the cognition of three dimensional construction of biological mark. For the rational drug design, structural information on both protein and ligand is necessary. In this attack, all of the available structural information is considered to better the ligand ‘s affinity by optimising its interaction with the protein mark. Recent surveies suggest that the influence of protein flexibleness and mobility are cardinal belongingss to be included in the drug design attacks. As Matrix Metalloproteinases ( MMP ‘s ) possess nomadic active sites, planing of their inhibitors is hard. This paper chiefly focuses on the influence of mobility of active sites of MMP on its drug design. Docking of MMP2 and MMP9 with its inhibitor Marimastat showed difference in interaction energy in instance of flexibleness of active site. From these observations, it is clear that the mobility is an of import facot which should be taken into consideration in instance of structure-based drug design for MMP.

Keywords: Structure – based drug design, mobility of active site, docking, MMP


Structure based drug design or direct drug design depends on the three dimensional construction of biological mark. In this technique, campaigner drugs that can adhere with high selectivity and affinity to the mark can be designed utilizing construction of mark. This method can be divided into two classs viz. ligand-based drug design and receptor -based drug design. Former is about happening ligands for a given receptor in which a figure of ligands are screened to happen those suiting the adhering pocket of receptor. Latter is by constructing ligands within the restraints of adhering pocket of receptor and therefore fresh construction can be obtained. This paper deals with construction based drug design for MMP ‘s.

Matrix Metalloproteinases ( MMP ‘s ) are zinc dependent endopeptidases involved in extracellular matrix and cellar membrane debasement. This household of protein consists of about 26 endopeptidases with conserved sphere constructions. MMP ‘s have function in different types of pathology chiefly tissue devastation in arthritic arthritis, degenerative arthritis, stomachic ulcer, malignant neoplastic disease invasion and metastasis, fibrosis in liver cirrhosis and multiple induration, weakening of matrix in aortal aneurism and restenotic lesion. MMP ‘s are classified based on the substrate specificity and cellular localization.They are involved in the cleavage of cell surface receptors, release of apoptotic ligands. They besides play major function in programmed cell death, distinction, cell proliferation, migration and host defense mechanism. Man-made MMP inhibitors can be developed by structure-based drug design. Adhering pockets or active site of MMP possess an built-in mobility. Therefore for the design of inhibitors for assorted MMP this mobility is taken into consideration.

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Mobility of active site is the beginning for receptor malleability and enables the adhering spouses or ligands to conformationally accommodate to each other. Receptor mobility is non merely limited to steric complementarity, but besides extra energetic and entropic parts may originate due to the binding affinity. Mobility of active site of receptor leads to a disfavorable reorganisation energy that may be big, even for preorganized binding sites. Configurational information parts result from the alterations in the receptor flexibleness upon complex formation. If flexibleness is transferred to other protein parts, it leads to the redistribution of protein configurational information. Configurational information can be computed by MD simulation. Transporting out interactive surveies between MMP and its inhibitor will assist to analyze about the influence of protein mobility on drug design.


Molecular Dynamics ( MD ) simulation is one of the most accurate computational techniques used in the field of macromolecular calculation. MD simulation has been utilized for the finding of receptor malleability which contributes to structure-based drug design. Informations related to structure-based drug design that can be analyzed with this include flexibleness and mobility, bring forthing multiple conformations of a protein, analyzing the influence of mutations and look intoing allosteric mechanisms. Atomistic simulation techniques such as molecular kineticss ( MD ) have become a powerful tool in the field of nanotechnology as they provide a physical penetration in understanding assorted phenomena on atomic graduated table and enable one to foretell some belongingss of nanomaterials. The simulation is performed over a period of clip utilizing good defined mathematical estimates of the known natural philosophies of atomic interactions. MD allows a user to examine the interactions of atoms, at the atomic graduated table, in molecules, on surfaces and in bulk solids. The complete MD computation procedure is multidisciplinary, where the relevant MD theory is good established from a mathematics, natural philosophies, and chemical science point of position. Furthermore, it employs computational algorithms developed from computing machine scientific discipline and information theory, which provide speedy and efficient numerical solutions. The MD method is normally used today in Fieldss, such as stuffs technology and biomolecular research.

The molecular kineticss simulation method is based on Newton ‘s 2nd jurisprudence or the equation of gesture, F=ma, where F is the force exerted on the atom, m is its mass and a is its acceleration. Knowing the force on each atom, it is possible to find the acceleration of each atom in the system. Integration of the equations of gesture so yields a flight that describes the places, speeds and accelerations of the atoms as they vary with clip. From this flight, the mean values of belongingss can be determined. The method is deterministic ; one time the places and speeds of each atom are known, the province of the system can be predicted at any clip in the hereafter or the past. Molecular kineticss simulations can be clip devouring and computationally expensive.

Newton ‘s equation of gesture is given by

Where Fi is the force exerted on atom I, myocardial infarction is the mass of atom I and Army Intelligence is the acceleration of atom I.

The force can besides be expressed as the gradient of the possible energy

Uniting these two equations outputs

where V is the possible energy of the system.

The simplest pick of V is to compose it as a amount of brace wise interactions:

The clause J & A ; gt ; I, in the 2nd summing up has the intent of sing each brace wise interaction merely one time.

Newton ‘s equation of gesture can so associate the derived function of the possible energy to the alterations in place as a map of clip.

Taking the simple instance where the acceleration is changeless

obtained an look for the speed after integrating

and since

we can one time once more incorporate to obtain

Uniting this equation with the look for the speed, the undermentioned relation is obtained which gives the value of ten at clip T as a map of the acceleration, a, the initial place, x0, and the initial speed, v0.

The acceleration is given as the derived function of the possible energy with regard to the place, R,

Therefore, to cipher a flight, one merely needs the initial places of the atoms, an initial distribution of speeds and the acceleration, which is determined by the gradient of the possible energy map. The equations of gesture are deterministic, e.g. the places and the speeds at clip zero find the places and speeds at all other times t. The initial places can be obtained from experimental constructions, such as the x-ray crystal construction of the molecule.

Docking is a Lock and Key procedure which predicts the preferable orientation of receptor to a ligand when edge to each other to organize a stable composite. It is used to foretell the binding orientation of drug campaigners to the protein marks. Hence docking dramas an of import function in the rational drug design. There are different types of moorage tools in Accelrys Discovery Studio chiefly CDOCKER, LigandFit and Flexible Docking.

CDOCKER is a molecular moorage method that employs CHARMm forcefield. Here the receptor is held stiff and ligand is flexible. For each airs CDOCKER energy and interaction energy have been calculated. LigandFit docking based on initial form lucifer to the binding site. Dock mark and ligand internal energy is obtained and therefore ligand interaction energy is calculated. Flexible moorage allows flexibleness of receptor during moorage of flexible ligands. The side-chains of amino acids in the active site are moved during docking leting the receptor to accommodate to ligands in induced-fit theoretical account. CDOCKER energy and CDOCKER interaction energy is obtained for each airs.


The MMP proteins – MMP2 and MMP9 – nowadays in homo were collected from Protein Data Bank. These proteins have been subjected to sequence and structural analysis. The primary construction analysis done utilizing ProtParam and the parametric quantities computed from the tool include the molecular weight, aminic acid composing, theoretical pi, estimated half life, instability index, aliphatic index and expansive norm of hydropathicity. The secondary construction analysis done with SOPMA from which the per centum of alpha spiral, beta bend and random spiral were obtained. The minimisation of the protein structures has been done utilizing Accelrys Discovery Studio at the molecular mechanics level utilizing CHARMm forcefield. Potential energy, Van der Waals energy, and RMS gradient values were computed. Electrostatic energy of the proteins was computed utilizing MGL Tool in Python Molecule Viewer.

The surface scanning of the proteins was carried out utilizing Computed Atlas of Surface Topography of Proteins ( CASTp ) tool. To imitate the kineticss behavior, the proteins were subjected to Dynamics ( Heating or Cooling ) protocol in Accelrys Discovery Studio. The protein construction obtained after Dynamics ( Heating or Cooling ) was once more scanned with CASTp to find the fluctuation in the surface construction.

The chemical construction of the drug Marimastat for MMP was obtained from DrugBank and it was optimized with Accelrys Material Studio. As Marimastat was given as the inhibitor of merely two isoforms of MMP – MMP2 and MMP9 – interaction surveies were done with these isoforms. Both stiff and flexible moorage was carried out for MMP2 and MMP9 with Marimastat utilizing CDOCKER, LigandFit and Flexible Docking tools of Accelrys Discovery Studio.


10 proteins of MMP, one for MMP2 ( 1RTG ) and nine for MMP9 ( 1GKC, 1GKD, 1ITV, 1L6J, 2OVX, 2OVZ, 2OW0, 2OW1, 2OW2 ) were retrieved. Consequences of ProtParam show that the proteins are hydrophilic in nature. It has been found that the proteins are stable in nature from the instability index values.1GKC and 1GKD was found to hold highest estimated half life. The secondary construction of protein chiefly consisted of random spirals, alpha spiral and beta bend.

Potential energy of the sculptural protein construction was extremely negative and exothermal for most of the proteins which implies high thermodynamic stableness. The Van der Waals energy was negative for all the proteins, bespeaking high possibility of secondary bonding. The RMS gradient is about 0, which indicates the stableness of protein construction. There was merely a little difference in electrostatic energy between the proteins, computed utilizing MGL.

The adhering pockets of protein analyzed utilizing CASTp. Number of pockets was more for 1ITV and 1GKC which indicates that they are less stable and position of mutant is high. Area and volume of the adhering pockets of 1L6J, 2OW1, 2OW0 and 2OW2 are more compared to other proteins bespeaking that their pockets are less heavy. Most of the binding pockets are hydrophilic in 1L6J, 2OW2, 2OW0, 2OVX, 1GKD, 2OW1, 2OVZ and 1ITV when compared to other proteins. CASTp analysis of the protein construction obtained after increasing the temperature to 312K and 314K by Dynamicss ( Heating or Cooling ) showed that the figure of adhering pockets increased for 1RTG, 1GKD, 2OVZ, 2OW2 and 1L6J.

Interaction surveies done for all the 10 proteins with optimized construction of Marimastat utilizing CDOCKER, LigandFit and Flexible Docking. Consequence showed that there is a difference in interaction energy and figure of airss for the proteins in different types of moorage. Interaction energies for the proteins for which there is a important difference in moorage is shown in the table-1

Table 1 Interaction surveies of proteins with Marimastat



Flexible Docking







































































From the consequences it is clear that Flexible Docking is holding higher figure of airss compared to CDOCKER and LigandFit. Interaction energies are most negative for CDOCKER in instance of 1L6J, 2OVZ, 2OW1 and 2OW2 and therefore are most favorable to adhering. As flexibleness of the active site of receptor additions, it influences the interaction between the ligand and the receptor.



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