Small molecules are used as inhibitors of protein action - as drugs. They most often do thisby blocking the active site within the protein. Potential drugs can be screenedcomputationally to determine if they are strongly bound to the protein.Figure 1 shows a possible conformation of a candidate drug molecule, 4-bromo-2-carboxymethylamide-pyrrole (abbreviation: BCMAP) at the active site of a protein(abbreviation: PR). Figure 2 shows the full protein structure whilst figure 3 shows a knowninhibitor of the protein at the site, overlayed with another calculated conformer of BCMAP.(c) Outline how you would investigate whether BCMAP would be an effective inhibitorfor the protein in competition with the molecules that the protein normally targets,and any solvent.Figure 1. 4-bromo-2-carboxymethylamide-pyrrole (BCMAP) (C, N, O, and Br atoms in yellow, blue,red, and brown, respectively) in the active site of the protein structure. Figure 2. Cartoon (ribbon) structure of the entire protein with a known inhibitor in position, asdetermined experimentally. Cations and water molecules in the protein structure are omitted forclarity. The links labelled can be cleaved chemically.lle1122CleavableLinksLeul120Tyr1167Asn1168Val1174Prol110Figure 3. An overlay of a known inhibitor (from Figure 2) and an example conformer of BCMAP. Dashedlines indicate hydrogens bonds and electrostatic interactions. The isolated cyan atoms are sodiumcations and the isolated red atoms the determined positions of the oxygen in a water molecule.

Inhibitors are the molecules that slow down or completely block the protein activity of molecules,…

Answered: (c) Outline how you would investigate…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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Prepare a schematic diagram and present it. The Figure should illustrate the interactions made between the key components of total and non-specific binding reactions in drug bindings. In preparing this figure, it should reflect on the role of each of the components of the reaction mixtures, and why the subtraction of non-specific from total binding allows us to calculate specific binding. The Figure Legend should be brief but informative.
From a medicinal chemistry (and a pharmacologist) perspective, functional groups provide specific properties and behaviors that allow drug molecules to exert their desired PD and PK effects. The key point here is that each individual group within a drug molecule can serve to provide one or more specific roles, tasks, or functions. The following table summarizes a series of drug discovery lead optimization for targeting a certain renal disease. Explain the basis for changing the R- functionality at the para- position. Please explain in as much detail as you need and by using scientific justifications, which one of the 4 candidates (526-529), presents the most viable investigational drug candidate, given the information provided below? N- `N' 'N' R- Drug Code R IC30 (nM) Half-Life (tı2), Minutes 526 CH;O 104 6 527 CF;0 1110 95 528 CH;CH, 11 <5 529 CH,CF, 14 96
Which of these heterocyclic drugs is likely to be the least soluble in water? Use the Fsp³ parameter to decide. OH Tramadol Chemical Formula: C16H25NO2 YOUR OW Pantoprazole Torasemide Chemical Formula: C16H15F2N3O4S Chemical Formula: C16H20N4O3S Temazepam -OH Chemical Formula: C16H13CIN₂O2 Tioconazole Chemical Formula: C16H13C3N₂OS A. Tramadol B. Pantoprazole C. Torasemide D. Temazepam E. Toconazole
Data from enzyme inhibition are used to determine a Kmapp and Vmax PP. Comparison of these values with assays run without inhibitor are used to understand how the inhibition is occurring. This is useful for better understanding the active site as well as the practical aspect of pharmaceutical drugs. Below are idealized Line-Weaver Burke plots of different types of inhibitors. Comnetitive Uncomnetitive Mixed +Inh +Inh 4Inh Anh Inh Anh [S] [S] [S] a. How does the value of Vmax for the enzyme compare to the Vmax PP of the inhibited enzyme for: i. Competitive ii. Uncompetitive iii. Mixed b. How does the value of Km for the enzyme compare to the Km PP of the inhibited enzyme for: i. Competitive ii. Uncompetitive iii. Mixed c. For each situation in Model 1, consider an inhibitor that is better than the one shown on the graph. Answer the following questions for each type of inhibition: i. How would the KmPP change? ii. How would the Vmax PP change?
Polyethylene glycol (PEG)-conjugated IFNs have superior pharmaceutical properties compared with their unconjugated counterparts as a result of greater protection against proteolytic degradation, better solubility, and slower catabolism and excretion. Group of answer choices True False
A schematic representation of the enzyme IspD complexed to inhibitor 3, and a series of inhibitors 3-5 are shown below. Ala202 lle240 mwww NH NH Val263 ОН www HN N- lle177 HN 'N' CI 3 X = N 4 X = C-CN 5 X = C-COO IC50 274 µM IC50 140 nM IC50 35 nM NH2 HN Val266 N -N O-H---- N HN %3D Arg157 HN wwww lle265 Explain why structure 4 is a more potent inhibitor (lower IC50 value) than inhibitor 3 and why structure 5 is a much weaker inhibitor (higher IC50 value) than 3 and 4.
(1) Discuss the structure and function of ion channels and describe their importance in medicinal chemistry. (ii) Draw the molecular structure of tamoxifen and discuss, in detail, its mode of therapeutic activity. Use the protein databank (PDB entry: 3ERT) to help support your answer.
what possible outcome may be produced when the molecular weight of an alcohol antiseptic is increase to a C20, will it still be effective? Explain your answer
3CLpro is a cysteine protease, which are among the most common proteases in biochemistry, however they are a structurally diverse family of enzymes especially in the organization of the active site amino acids. A group of scientists have reported a potential drug molecule based on a binding study using circular dichroism. They report that the molecule binds to the active site. Can the experiment support the claims, why or why not? Which techniques might be used to support this claim?
A tetrapeptide, glutamate-glycine-alanine-lysine, is prepared at at concentration of 1 mM (0.001 M) and is measured in the standard setup (pathlength of 1 cm). What is the approximate absorbance of this peptide at 280 nm? Hint: if the peptide contained a single tryptophan, the answer would be about 10. 10 280 1 0
The following structure is more active than morphine as an analgesic. H3C CH3 H. H3C' O Il.. What is the principal reason for this? The extra acetyl group binds to cell surface receptors improving active internalization. The acetyl groups mask a polar group allowing the structure to cross the blood brain barrier more efficiently. The extra acetyl group masks an alcohol group which would otherwise undergo a phase Il metabolic conjugation reaction leading to rapid excretion of the drug. The acetyl groups increase the stability of the drug in the cellular environment. O Il..
H CH₂ H₂C HC-CH3 CH₂ H H₂C (S) H₂C H CH₂ CH₂ CH₂ NH O C NH NH₂ a) Which of the following statements about this peptide are correct? Group of answer choices Treatment of this peptide with trypsin generates two products. This peptide is a substrate for carboxypeptidase A Treatment of this peptide with cyanogen bromide generates a pentapeptide and a tripeptide. Treatment of this peptide with chymotrypsin generates three products. Treatment of this peptide with elastase generates 2 products. None of the above statements are correct. b) What is the sequence of this peptide using one letter abbreviations? c) What is the pH which would correspond to the ionization of the peptide as drawn above? 1, 5, 7, 10, 14

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(c) Outline how you would investigate whether BCMAP would be an effective inhibitor for the protein in competition with the molecules that the protein normally targets, and any solvent.