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This is a piece of assessed coursework and should be submitted into the ‘Coursework’ folder on WebLearn within Online Assessments.

In the table below, you have been designated a compound, which is known to act as an inhibitor for one (or more enzymes).

Describe in detail:

  • the structure and role of the compound
  • the action of the enzyme (for those compounds that act as inhibitors for more than one enzyme, choose only one)
  • its role in acting as an inhibitor to the enzyme (including the type of inhibition N.B. this may be irreversible (also known as suicide), competitive, non competitive, uncompetitive or mixed)

As below, with a greater insight/originality and wider/deeper engagement with the literature

  • Authoritative grasp of inhibition theory/concepts, method and context
  • Comprehensive integration of up-to-date literature and data
  • Very well structured and referenced using an appropriate style
  • Insight or originality in the way the topic is developed and presented including an effective use of diagrams/figures
  • Demonstrates innovation in communicating new ideas to an audience/ reader using an engaging style
  • Strong grasp of inhibition theory/concepts, method and context
  • Very good integration of up-to-date literature and data
  • Well-structured and referenced using an appropriate style
  • Very good integration of media and/or diagrams/figures
  • Demonstrates some originality in communicating concepts and engaging the audience/reader
  • Sound understanding of inhibition concepts and methods within context
  • Clear integration of literature and data referenced in an appropriate style
  • Effective use of media and/or diagrams/figures in communicating concepts to the audience/reader
  • Clearly presented with an appropriate structure
  • Decent grasp of basic inhibition concepts and methods within context
  • Some inclusion of literature and data that are referenced
  • Limited incorporation of diagrams/figures
  • Reasonably clearly presented and structured

Structure of Hirudin

It refers to a peptide that occurs naturally in the salivary glands of the blood-sucking leeches. The examples of such blood leeches include Hirudin medicinalis which is known to be having blood anticoagulant property. This property is very crucial for the alimentary habit of the hematophagy shown by the leeches considering that it keeps the blood flowing after the first operation of the phlebotomy is carried out on the skin of the host by the worm (Sellers et.al 2014).

During the times of the great scientists John Berry, there were publications of the paper that dealing with the coagulation of the blood. In his work, he discovered that the leech secreted a very powerful anticoagulant and he refers to the anticoagulant as the hirudin. The isolation of this structure was not done until the year 1950 with the determination of its full structure being finished on the year 1976.The full length of this structure is made up of roughly 65 amino acids.

The present amino acids are arranged in the form of a solid N-terminal domain possessing three disulphide bonds and a terminal of C. The C compound is perfectly disordered when the protein is subjected to the uncompleted solution. The residues of the amino acids normally form a parallel beta strand of 1-3 to the residues of thrombin 214-217.The ser-195 O gamma atom present in the site of the catalytic will form the hydrogen bond with the nitrogen atom of the residue 1. There are several electrostatic interactions between the C-terminal domain and the anion-binding of the thrombin exosite (Lu et.ai 2013)

 The last five residues form a loop that is helical and this results into hydrophobic contacts. There are several mixtures of the isoforms of the protein in the natural Rudin. The homogeneous preparation of the hirudin can be an achieved using a technique of the recombinant.

In the final stages of the coagulation of the blood, the most common activity is the conversion of the fibrinogen into the fibrin. This is done by an enzyme called serine protease thrombin. The production of the thrombin is from the prothrombin and this is facilitated by an enzyme called prothrombinase towards the end of the coagulation stages.

 The activity includes the use of the Factor Xa together with the Factor Va as the cofactor especially in the final stages of the coagulation. A blood clot is formed through linking of the fibrin by the factor XIII. The XIII is also known as the fibrin stabilizing factor. The primary inhibitor of the thrombin in the normal circulation of the blood is the antithrombin. The anticoagulant activity of the hirudin is based on its capability to inhibit the activity of the thrombin of procoagulation. This is what makes it similar to the antithrombin.

Mechanism of Action as a Thrombin Inhibitor

Hirudin is the primary natural inhibitor of the thrombin. It normally binds to and inhibit only the thrombin that ha been activated. This limits its activities to specifically on the fibrinogen’s hirudin therefore prevents the formation of the clots and the thrombi. This makes the activity to be a thrombolytic.

Hirudin has a therapeutic value in the blood coagulation disorders and in the treatment process of the skin hematomas together with the superficial varicose veins. It can be used either as an injection or as a cream to be applied. The advantage of the hirudin over other commonly used anticoagulant and thrombolytics like heparin is that it does not trigger any interference with the biological operations of the present serum proteins. Besides it can act as a very complexed thrombin.

The compounds such as lepirudin and desirudin are commonly known as the recombinant hirudin derivatives that inhibits directly free and fibrin bound thrombin thereby blocking its activities. There exist also a group of the derivatives such as Bivalirudin, argatroban among others that are synthetic. The derivatives of the hirudin and the hirudin itself acts as a bivalent direct thrombin inhibitor.

 The block both the active sites and the exosite. The Bivalirudin binds reversibly to the compound of the thrombin and this makes its inhibitory effect a transient which consequently results into the diminished risk of serious bleeding. The univalent direct thrombin inhibitors that binds only to the active sites of the thrombin includes the Argatroban and gabigatran etexilate. The approval of the gabigatran was done in the year 2012 as the first new direct oral anticoagulant treatment option. The use of the direct thrombin is common in the cases where there is intolerability of the heparin such as the heparin induced.

Recombinant hirudin does not have the sulfidation effects and this leads into a two-fold loss of potency without putting any change in its specificity of inhibiting thrombin. The crystallographic structure of X-ray details shows a structure of the hirudin-thrombin that are coupled in the complex manner (Strassel et.al 2012). The study of the structure indicates that the amino terminal domain of the hirudin interacts with the active sites of the thrombin’s catalytic triad residue. This is carried along with the carboxy terminal domain that binds positively to the charged anion binding exosite (Huang et.al 2012)

When an intravenous dose of hirudin is used, the commonly observed half-life is just 40minutes.This half-life is increased to a round 200 minutes with the injection of the subcutaneous. The excretion of the hirudin is predominantly done by the kidneys. There is a prolonged PPT in the dose-dependent manner.

Therapeutic Uses of Hirudin

The injection type of subcutaneous of 0.1mg/kg extends the prolong duration almost twice. However, when given to the volunteers Hirudin does not prolong the bleeding time twice with the recommended baseline. The studies have shown that the patients with the coronary arterial and the venous thrombosis have slight decrease in the angioplasty-associated acute complications with higher risks of bleeding (Guo-Qian, Gang and Zhi-Yong 2012)

It is however, beneficial in the long term. Hirudin has been shown to be slightly better as compared to heparin in the prevention of the thromboembolism of the venous especially with the patients that are undergoing the replacement of the hip. This advantage extends even to the treatment of the established deep vein thrombosis.

QUESTION TWO

(a)The intermediaries present in the reactions include substrate and the enzymes.

 (b)    X=(E)+(EH)+(EHs)

      Y=(Es)+(EHS) +(EHP) +(EH2P)

       Z=(EP)+(EHP)+(EHP) the overall expression thus becomes x+y+z=(Es).

(c) For a given reaction aA +bB=C, the rate of reaction was taken as r=K(A)a (B)b in which k=reaction rate, (A) concentration of A and the concentration of B respectively. Using the above equation;

 X=(E)+(EH)+(EHs)

 Y=(Es)+(EHS) +(EHP) +(EH2P)

  Z=(EP)+(EHP)+(EHP) the overall expression thus becomes x+y+z=(Es).

1/V0=Km/Vmax(1+[I]/K1) x1/[S]+1/Vmax(1+[I]/K1) and this give the value of Km/Vmax(1+{I]/K1) = 1132.1 which corresponds to K1=4.1x10-3M

(d)The rate law of the reaction can be obtained using the isolation method of the reactants. In this      particular case the reactant used taken as A+B=Consider Both be in excess in this reaction and so taking the concentration of b to be constant, the law of expression becomes V=K(A) K’=K(B)0

(e) When the Concentration of the substrate is taken to be very low. The reaction will shift to the left and this results into the reduced value of the product. In this particular reaction, other factors that affect reaction apart from the PH are held constant. This includes the temperature and pressure (Xu et.al 2013).

QUESTION 3

  • It states that the rate of the enzymatic reaction in which the substrate S is converted into the product P depends on the concentration of the enzyme despite the fact that the enzyme doe not undergo any change.

(b)Determination of the values of Km and Vmax of the enzymes.

According to the graph, the inhibitor A and B, meets at the X-axis thus non-competitive type of inhibitors. The graphical determination is as shown below

The line with no inhibition crosses the axis of Y at 2.5x105M-1s and this translates to a Vmax 6.12x10-6MS-1. The gradient of the line Km /Vmax=1.88x10-4M (Greinacher2012)

(c) Determination of the type of the inhibition

Since this has been established for the competitive inhibitor;

1/Vo=Km/Vmax(1+[1]/K1) x1/[S]+1/Vmax.

The slope for the competitive inhibitor=Km/Vmax(1+1/K1) =901.6

Substituting for the value of the gradient which 297 and taking int assumptions that [I] is 8.0x10-3Ms, the resultant value of K1 =6.6x10-3M.

Also taking the formula for the calculation of the non-competitive inhibitor; (Yingxin et.al 2013)

1/V0=Km/Vmax(1+[I]/K1) x1/[S]+1/Vmax(1+[I]/K1) and this give the value of Km/Vmax(1+{I]/K1) = 1132.1 which corresponds to K1=4.1x10-3M

References

Greinacher, A., 2012. Recombinant 14 hirudin for the treatment of heparin-induced thrombocytopenia. Heparin-induced thrombocytopenia, p.388.

Guo-Qian, Y., Gang, W. and Zhi-Yong, S., 2012. Investigation on the microcirculation effect of local application of natural hirudin on porcine random skin flap venous congestion. Cell biochemistry and biophysics, 62(1), pp.141-146.

Huang, Y., Zhang, Y., Wu, Y., Wang, J., Liu, X., Dai, L., Wang, L., Yu, M. and Mo, W., 2012. Expression, purification, and mass spectrometric analysis of 15N, 13C-labeled RGD-hirudin, expressed in Pichia pastoris, for NMR studies. PLoS One, 7(8), p. e42207.

Lu, W., Cai, X., Gu, Z., Huang, Y., Xia, B. and Cao, P., 2013. Production and characterization of hirudin variant-1 by SUMO fusion technology in E. coli. Molecular biotechnology, 53(1), pp.41-48.

Sellers, D.L., Kim, T.H., Mount, C.W., Pun, S.H. and Horner, P.J., 2014. Poly (lactic-co-glycolic) acid microspheres encapsulated in Pluronic F-127 prolong hirudin delivery and improve functional recovery from a demyelination lesion. Biomaterials, 35(31), pp.8895-8902.

Strassel, C., Eckly, A., Léon, C., Moog, S., Cazenave, J.P., Gachet, C. and Lanza, F., 2012. Hirudin and heparin enable efficient megakaryocyte differentiation of mouse bone marrow progenitors. Experimental cell research, 318(1), pp.25-32.

Xu, Y., Wu, W., Wang, L., Chintala, M., Plump, A.S., Ogletree, M.L. and Chen, Z., 2013. Differential profiles of thrombin inhibitors (heparin, hirudin, bivalirudin, and dabigatran) in the thrombin generation assay and thromboelastography in vitro. Blood Coagulation & Fibrinolysis, 24(3), pp.332-338.

Yingxin, G., Guoqian, Y., Jiaquan, L. and Han, X., 2013. Effects of natural and recombinant hirudin on VEGF expression and random skin flap survival in a venous congested rat model. International surgery, 98(1), pp.82-87.

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