# Computer-Aided Design of Peptidomimetic Inhibitors of Falcipain-3: QSAR and Pharmacophore Models

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## Abstract

**:**

_{com}) and the experimentally measured ${\mathrm{IC}}_{50}^{\mathrm{exp}}$. Apart from the structure-based relationship, a ligand-based quantitative pharmacophore model (PH4) of novel PEP analogues where substitutions were directed by comparative analysis of the active site interactions was derived using the proposed bound conformations of the PEPx. This provided structural information useful for the design of virtual combinatorial libraries (VL), which was virtually screened based on the 3D-QSAR PH4. The end results were predictive inhibitory activities falling within the low nanomolar concentration range.

## 1. Introduction

## 2. Materials and Methods

#### 2.1. Biological Activities of Compounds Included in the Training and Validation Sets

#### 2.2. Molecular Modeling

#### 2.3. Molecular Mechanics

#### 2.4. Conformational Search

#### 2.5. Solvation Gibbs Free Energy

#### 2.6. Calculation of the Entropic Term

#### 2.7. Binding Affinity Calculations

#### 2.8. Interaction Energy Calculations

#### 2.9. Pharmacophore (PH4) Modeling

#### 2.10. Generation of the Virtual Library

^{−5}Å and a dielectric constant of 4 using the CHARMm force field were set, as described in Section 2.3.

#### 2.11. In Silico Screening

## 3. Results and Discussion

#### 3.1. Selection of Training and Validation (or Test) Data Sets

#### 3.2. Obtained QSAR Model

#### 3.3. Inhibitor Binding Modes

#### 3.4. Ligand-Based 3D-QSAR PH4 Model of FP3 Inhibition

^{2}) falls to an interval from 0.90 to 0.99. The first PH4 hypothesis with the best RMSD and R

^{2}was retained for further analysis. The statistical data for the set of hypotheses (costs, RMSD, R

^{2}) are listed in Table 4. The geometry of the Hypo1 pharmacophore of FP3 inhibition is displayed in Figure 5. Table 5 lists the regression equation (Table 3) for ${\mathrm{pIC}}_{50}^{\mathrm{exp}}$ vs. ${\mathrm{pIC}}_{50}^{\mathrm{pre}}$ estimated from Hypo1 with related indicators such as ${\mathrm{R}}^{2}$, ${\mathrm{R}}_{\mathrm{xv}}^{2}$, Fisher F-test, $\sigma $ and $\alpha $, while Figure 6 displays a plot of regression equation for ${\mathrm{pIC}}_{50}^{\mathrm{exp}}\mathrm{vs}.{\mathrm{pIC}}_{50}^{\mathrm{pre}}$. To check the consistency of the generated pharmacophore model, we have computed the ratio of predicted and observed activities $({\mathrm{pIC}}_{50}^{\mathrm{pre}}/({\mathrm{pIC}}_{50}^{\mathrm{exp}}$) for the validation set. The computed ratios are as follows: PEP26 (1.01), PEP28 (1.01), PEP36 (1.01) all of them relatively close to one, which documents the substantial predictive power of the regression for the best PH4 model.

#### 3.5. Library Design and ADME Focusing

_{1}to R

_{4}of the appropriate scaffold to provide a combinatorial library of the size: ${\mathrm{R}}_{1}\times {\mathrm{R}}_{2}\times {\mathrm{R}}_{3}\times {\mathrm{R}}_{4}={19}^{4}=130,321$ PEPAs.

#### 3.6. Screening PEPs Virtual Library Using the Obtained in Silico Model

#### 3.7. Analysis of New Inhibitors

## 4. Conclusions

## Author Contributions

## Funding

## Data Availability Statement

## Acknowledgments

## Conflicts of Interest

## References

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**Figure 1.**Chemical structures of training and validation sets of FP3 inhibitors obtained from literature [24].

**Figure 2.**Correlation plot between ${\mathrm{pIC}}_{50}^{\mathrm{exp}}$ and relative complexation Gibbs free energies $\u2206\u2206{\mathrm{G}}_{\mathrm{com}}$ of the training set of nine FP3 inhibitors.

**Figure 3.**Breakdown of interaction energy (kcal/mol) contribution between PEP32, PEP39, PEP40 and the most interacting residues of the FP3 active site.

**Figure 4.**Proposed binding mode of peptidomimetics inhibitors at the active site of FP3. Main favourable non-bond interactions depicted in 3D (

**left picture**) and 2D (

**right picture**) for the most active PEP39 (purple carbons atoms).

**Figure 5.**(

**a**) Features of the Hypo1 pharmacophore of FP3 inhibition; (

**b**) pharmacophore mapping by the most active of the training set PEP39; (

**c**) inter-features distances in Å; (

**d**) angles between features. Colours legend of features: hydrophobic (blue), hydrogen bond acceptor (green), hydrogen bond donor (purple), excluded volumes (grey).

**Figure 8.**The best virtual hit, analogue PEP-14-14-14-18 (with purple carbons atoms), mapped a PH4 Hypo 1.

**Figure 9.**Connolly surfaces (left) and 3D (right) schematic interaction diagrams of the 4 most potent analogues designed at the active site of PfFP3: (

**a**) PEP-17-03-14-10 (${\mathrm{IC}}_{50}^{\mathrm{pre}}$ = 0.29 nM); (

**b**) PEP-08-15-18-19 (${\mathrm{IC}}_{50}^{\mathrm{pre}}$ = 0.19 nM); (

**c**) PEP-13-06-04-19 (${\mathrm{IC}}_{50}^{\mathrm{pre}}$ = 0.10 nM); (

**d**) PEP-14-14-14-18 (${\mathrm{IC}}_{50}^{\mathrm{pre}}$= 0.07 nM).

**Table 1.**Training and validation sets of PEP inhibitors obtained from the literature [24].

Training Set ^{[a]} | ${\mathbf{M}}_{\mathbf{W}}{}^{\left[\mathbf{b}\right]}(\mathbf{g}\xb7{\mathbf{mol}}^{-1})$ | $\mathbf{I}{\mathbf{C}}_{50}^{\mathbf{exp}}{}^{\left[\mathbf{c}\right]}\left(\mathbf{nM}\right)$ |
---|---|---|

PEP23 (Ref) | 482.61 | 36,360 |

PEP27 | 452.56 | 910 |

PEP29 | 438.53 | 23,900 |

PEP32 | 466.54 | 47,230 |

PEP34 | 470.60 | 8220 |

PEP38 | 462.55 | 25,440 |

PEP39 | 440.50 | 60 |

PEP40 | 574.75 | 520 |

PEP41 | 498.61 | 3560 |

Validation Set ^{[a]} | ${M}_{W}$^{[b]}(g · mol^{−1}) | $I{C}_{50}^{exp}$^{[c]}(nM) |

PEP26 | 452.56 | 540 |

PEP28 | 450.54 | 20,180 |

PEP36 | 488.59 | 11,910 |

**Table 2.**Energy contributions towards $\u2206\u2206{\mathrm{G}}_{\mathrm{com}}$ for a dataset of PEP analogues against FP3 complexation Gibbs free energy and its components for the training and validation set of FP3 inhibitors. and experimental activity.

$\mathbf{T}\mathbf{r}\mathbf{a}\mathbf{i}\mathbf{n}\mathbf{i}\mathbf{n}\mathbf{g}\mathbf{S}\mathbf{e}\mathbf{t}{}^{\left[\mathbf{a}\right]}$ | $\mathbf{\u2206}\mathbf{\u2206}{\mathbf{H}}_{\mathbf{M}\mathbf{M}}{}^{\left[\mathbf{b}\right]}$ $\left(\mathbf{k}\mathbf{c}\mathbf{a}\mathbf{l}\xb7\mathbf{m}\mathbf{o}{\mathbf{l}}^{-1}\right)$ | $\mathbf{\u2206}\mathbf{\u2206}{\mathbf{G}}_{\mathbf{s}\mathbf{o}\mathbf{l}}{}^{\left[\mathbf{c}\right]}$ $\left(\mathbf{k}\mathbf{c}\mathbf{a}\mathbf{l}\xb7\mathbf{m}\mathbf{o}{\mathbf{l}}^{-1}\right)$ | $\mathbf{\u2206}\mathbf{\u2206}\mathbf{T}{\mathbf{S}}_{\mathbf{v}\mathbf{i}\mathbf{b}}{}^{\left[\mathbf{d}\right]}$ $\left(\mathbf{k}\mathbf{c}\mathbf{a}\mathbf{l}\xb7\mathbf{m}\mathbf{o}{\mathbf{l}}^{-1}\right)$ | $\mathbf{\u2206}\mathbf{\u2206}{\mathbf{G}}_{\mathbf{c}\mathbf{o}\mathbf{m}}{}^{\left[\mathbf{e}\right]}$ $\left(\mathbf{k}\mathbf{c}\mathbf{a}\mathbf{l}\xb7\mathbf{m}\mathbf{o}{\mathbf{l}}^{-1}\right)$ | $\mathbf{p}\mathbf{I}{\mathbf{C}}_{50}^{\mathbf{e}\mathbf{x}\mathbf{p}}{}^{\left[\mathbf{f}\right]}$ |
---|---|---|---|---|---|

PEP23 (Ref) | 0.00 | 0.00 | 0.00 | 0.00 | 4.44 |

PEP27 | −3.81 | −0.04 | -0.16 | −3.69 | 6.04 |

PEP29 | −0.39 | 0.13 | 1.45 | −1.71 | 4.62 |

PEP32 | 6.21 | −7.77 | -0.60 | −0.95 | 4.33 |

PEP34 | 5.97 | −9.92 | -0.51 | −3.44 | 5.09 |

PEP38 | 0.21 | 0.77 | 2.13 | −1.15 | 4.59 |

PEP39 | −2.07 | 0.12 | 3.98 | −5.92 | 7.22 |

PEP40 | −6.33 | 1.64 | 0.26 | −4.95 | 6.28 |

PEP41 | −3.24 | 1.16 | 0.42 | −2.50 | 5.45 |

$Validation$ $Set$ ^{[a]} | $\u2206\u2206{H}_{MM}$^{[b]}$\left(kcal\xb7mo{l}^{-1}\right)$ | $\u2206\u2206{G}_{sol}$^{[c]}$\left(kcal\xb7mo{l}^{-1}\right)$ | $\u2206\u2206{T}{S}_{vib}$^{[d]}$\left(kcal\xb7mo{l}^{-1}\right)$ | $\u2206\u2206{G}_{com}$^{[e]}$\left(kcal\xb7mo{l}^{-1}\right)$ | $Ratio$^{[g]} |

PEP26 | −7.67 | 1.39 | −0.78 | −5.50 | 1.07 |

PEP28 | −4.13 | 0.61 | −0.41 | −3.12 | 1.18 |

PEP36 | 6.51 | −10.30 | −0.15 | −3.64 | 1.18 |

^{[a]}For the chemical structures of the training/validation set of inhibitors see Figure 1.

^{[b]}$\u2206\u2206{\mathrm{H}}_{\mathrm{MM}}$ represents the relative enthalpic contribution to the Gibbs free energy change related to the intermolecular interactions in the enzyme–inhibitor complex derived by molecular mechanics (PEP23 (Ref) is the reference inhibitor ${\mathrm{I}}_{\mathrm{ref}}$):$\u2206\u2206{\mathrm{H}}_{\mathrm{MM}}=\left[{\mathrm{E}}_{\mathrm{MM}}\left\{\mathrm{E}:{\mathrm{I}}_{\mathrm{x}}\right\}-{\mathrm{E}}_{\mathrm{MM}}\left\{{\mathrm{I}}_{\mathrm{x}}\right\}\right]-\left[{\mathrm{E}}_{\mathrm{MM}}\left\{\mathrm{E}:{\mathrm{I}}_{\mathrm{ref}}\right\}-{\mathrm{E}}_{\mathrm{MM}}\left\{{\mathrm{I}}_{\mathrm{ref}}\right\}\right]\left(10\right)$.

^{[c]}$\u2206\u2206{\mathrm{G}}_{\mathrm{sol}}$ represents the relative solvation GFE contribution to the GFE of EI complex formation: $\u2206\u2206{\mathrm{G}}_{\mathrm{sol}}=\left[{\mathrm{G}}_{\mathrm{sol}}\left\{\mathrm{E}:{\mathrm{I}}_{\mathrm{x}}\right\}-{\mathrm{G}}_{\mathrm{sol}}\left\{{\mathrm{I}}_{\mathrm{x}}\right\}\right]-\left[{\mathrm{G}}_{\mathrm{sol}}\left\{\mathrm{E}:{\mathrm{I}}_{\mathrm{ref}}\right\}-{\mathrm{G}}_{\mathrm{sol}}\left\{{\mathrm{I}}_{\mathrm{ref}}\right\}\right]\left(11\right).$

^{[d]}$\u2206\u2206{\mathrm{TS}}_{\mathrm{vib}}$ represents the relative entropic contribution of the inhibitor to the GFE related to the E:I complex:$\u2206\u2206{\mathrm{TS}}_{\mathrm{vib}}=\left[\u2206\u2206{\mathrm{TS}}_{\mathrm{vib}}{\left\{{\mathrm{I}}_{\mathrm{x}}\right\}}_{\mathrm{E}}-\u2206\u2206{\mathrm{TS}}_{\mathrm{vib}}\left\{{\mathrm{I}}_{\mathrm{x}}\right\}\left]-\right[\u2206\u2206{\mathrm{TS}}_{\mathrm{vib}}{\left\{{\mathrm{I}}_{\mathrm{ref}}\right\}}_{\mathrm{E}}-\u2206\u2206{\mathrm{TS}}_{\mathrm{vib}}\left\{{\mathrm{I}}_{\mathrm{ref}}\right\}\right]\left(12\right)$.

^{[e]}$\u2206\u2206{\mathrm{G}}_{\mathrm{com}}$ represents the relative GFE change related to the enzyme-inhibitor complex formation: (see Equation (9)).

^{[f]}${\mathrm{IC}}_{50}^{\mathrm{exp}}$ [24] represents the inhibitor concentration that causes 50% decrease in the rate of substrate conversion by FP3 measured in the enzyme assay: ${\mathrm{pIC}}_{50}^{\mathrm{exp}}=-{\mathrm{log}}_{10}\frac{{\mathrm{IC}}_{50}^{\mathrm{exp}}}{{10}^{9}}$.

^{[g]}This is the ratio of the predicted activity on the experimental activity, ${\mathrm{pIC}}_{50}^{\mathrm{pre}}/{\mathrm{pIC}}_{50}^{\mathrm{exp}}$. This ratio is close to 1, indicating the predictivity of the QSAR model.

**Table 3.**Statistical data of correlation between computed $\u2206\u2206{\mathrm{G}}_{\mathrm{com}}$ ${\mathrm{IC}}_{50}^{\mathrm{exp}}$ of the training set.${\mathrm{pIC}}_{50}^{\mathrm{exp}}=-{\mathrm{log}}_{10}\left({\mathrm{IC}}_{50}^{\mathrm{exp}}\times {10}^{-9}\right)=-0.4794\times \u2206\u2206{\mathrm{G}}_{\mathrm{com}}+4.0455$.

Statistical Data of Linear Regression | |
---|---|

Number of compounds n | 9 |

$\mathrm{Squared}\mathrm{correlation}\mathrm{coefficient}\mathrm{of}\mathrm{regression}{\mathrm{R}}^{2}$ | $0.89$ |

$\mathrm{Leave}-\mathrm{one}-\mathrm{out}\mathrm{cross}-\mathrm{validated}\mathrm{squared}\mathrm{correlation}\mathrm{Coefficient}{\mathrm{R}}_{\mathrm{xv}}^{2}$ | $0.81$ |

$\mathrm{Standard}$ | $0.34$ |

Statistical significance of regression, Fisher F-test | 58.58 |

Level of statistical significance α | $>95\%$ |

$\mathrm{Range}\mathrm{of}\mathrm{activities}\mathrm{of}{\mathrm{IC}}_{50}^{\mathrm{exp}}$(nM) | 60–47,230 |

**Table 4.**Output parameters of 10 generated PH4 pharmacophoric hypotheses for FP3 inhibitors after Cat-Scramble validation procedure (49 scrambled runs for each hypothesis at the selected level of confidence of 98%).

Hypothesis | RMSD ^{[a]} | R^{2 [b]} | Total Costs ^{[c]} | Costs Difference ^{[d]} | Closest Random ^{[e]} |
---|---|---|---|---|---|

Hypo 1 | 0.795 | 0.999 | 24.13 | 2293.1 | 31.20 |

Hypo 2 | 2.958 | 0.991 | 60.64 | 2256.6 | 31.90 |

Hypo 3 | 3.623 | 0.987 | 80.35 | 2236.9 | 39.75 |

Hypo 4 | 4.907 | 0.976 | 130.37 | 2186.9 | 42.21 |

Hypo 5 | 5.128 | 0.974 | 139.89 | 2177.4 | 44.21 |

Hypo 6 | 5.203 | 0.973 | 143.71 | 2173.5 | 45.02 |

Hypo 7 | 5.880 | 0.966 | 177.49 | 2139.8 | 45.02 |

Hypo 8 | 7.910 | 0.937 | 304.23 | 2013.0 | 45.03 |

Hypo 9 | 9.767 | 0.902 | 451.68 | 1865.6 | 46.00 |

Hypo 10 | 9.830 | 0.901 | 456.44 | 1860.8 | 47.18 |

^{[a]}root mean square deviation;

^{[b]}squared correlation coefficient;

^{[c]}overall cost parameter of the PH4 pharmacophore;

^{[d]}cost difference between null cost and hypothesis total cost;

^{[e]}lowest cost from 49 scrambled runs at a selected level of confidence of 98%. The fixed cost = 21.24, with RMSD = 0, the null cost = 2317.26, with RMSD = 22.65 and the configuration cost = 11.85.

**Table 5.**Statistical data on regression analysis of correlation for the training set between PH4 predicted activity (${\mathrm{pIC}}_{50}^{\mathrm{pre}}$ ) and experimental one (${\mathrm{pIC}}_{50}^{\mathrm{exp}}$) against FP3.${\mathrm{pIC}}_{50}^{\mathrm{exp}}=-{\mathrm{log}}_{10}\left({\mathrm{IC}}_{50}^{\mathrm{exp}}\times {10}^{-9}\right)=1.0002\times {\mathrm{pIC}}_{50}^{\mathrm{pre}}-0.0012$.

Statistical Data of Linear Regression | |
---|---|

Number of compounds n | 9 |

$\mathrm{Squared}\mathrm{correlation}\mathrm{coefficient}\mathrm{of}\mathrm{regression}{\mathrm{R}}^{2}$ | $0.99$ |

$\mathrm{Leave}-\mathrm{one}-\mathrm{out}\mathrm{cross}-\mathrm{validated}\mathrm{squared}\mathrm{correlation}\mathrm{Coefficient}{\mathrm{R}}_{\mathrm{xv}}^{2}$ | $0.$99 |

$\mathrm{Standard}$ | 0.04 |

Statistical significance of regression, Fisher F-test | 5675.56 |

Level of statistical significance α | $>98\%$ |

$\mathrm{Range}\mathrm{of}\mathrm{activities}\mathrm{of}{\mathrm{IC}}_{50}^{\mathrm{exp}}$(nM) | 60–47,230 |

**Table 6.**R-groups (amino acid side chains) used in the design of the initial diversity library of PEP analogues. Dashed bonds indicate the attachment points of the fragments.

1 [Gly] | –H | 2 [Ala] | –CH_{3} | 3 [Val] | –CH(CH_{3})_{2} | 4 [Leu] | –CH_{2}-CH(CH_{3})_{2} |

5 [Ile] | –C(CH_{3})–C_{2}H_{5} | 6 [Met] | –-(CH_{2})_{2}–S–CH_{3} | 7 [Cys] | –CH_{2}–SH | 8 [Ser] | –CH_{2}–OH |

9 [Thr] | –CH(OH)-CH_{3} | 10 [Asp] | –CH_{2}–COOH | 11 [Glu] | –(CH_{2})_{2}–COOH | 12 [Asn] | –CH_{2}–CONH_{2} |

13 [Gln] | –(CH_{2})_{2}–CONH_{2} | 14 [Lys] | –(CH_{2})_{4}–NH_{2} | 15 [Arg] | –(CH_{2})_{3}–NH–C(NH)-NH_{2} | 16 [His] | |

17 [Phe] | 18 [Tyr] | 19 [Trp] |

**Table 7.**Complexation Gibbs free energy and its components for the top 21 scoring virtually designed analogues. The analogue numbering concatenates the index of each substituent R1 to R4 numbered in Table 6.

Analogues ^{[a]} | ${\mathbf{M}}_{\mathbf{W}}{}^{\left[\mathbf{b}\right]}$ | $\mathbf{\u2206}\mathbf{\u2206}{\mathbf{H}}_{\mathbf{M}\mathbf{M}}{}^{\left[\mathbf{c}\right]}$ | $\mathbf{\u2206}\mathbf{\u2206}{\mathbf{G}}_{\mathbf{s}\mathbf{o}\mathbf{l}}{}^{\left[\mathbf{d}\right]}$ | $\mathbf{\u2206}\mathbf{\u2206}\mathbf{T}{\mathbf{S}}_{\mathbf{v}\mathbf{i}\mathbf{b}}{}^{\left[\mathbf{e}\right]}$ | $\mathbf{\u2206}\mathbf{\u2206}{\mathbf{G}}_{\mathbf{c}\mathbf{o}\mathbf{m}}{}^{\left[\mathbf{f}\right]}$ | $\mathbf{I}{\mathbf{C}}_{50}^{\mathbf{p}\mathbf{r}\mathbf{e}}\left(\mathbf{nM}\right){}^{\left[\mathbf{g}\right]}$ |
---|---|---|---|---|---|---|

PEP23 | 482.61 | 0.00 | 0.00 | 0.00 | 0.00 | 36,360 |

PEP-14-19-04-01 | 400.53 | 5.54 | −6.82 | 0.75 | −2.03 | 9580.30 |

PEP-15-04-17-01 | 389.50 | −1.05 | −6.59 | 0.72 | −8.36 | 8.76 |

PEP-15-04-18-01 | 405.50 | −4.11 | −1.27 | 1.32 | −6.69 | 55.75 |

PEP-05-12-19-03 | 428.54 | −5.96 | 1.25 | 1.43 | −6.14 | 102.41 |

PEP-15-04-17-03 | 431.58 | −6.25 | −2.27 | 2.78 | −11.30 | 0.34 |

PEP-18-05-14-03 | 419.57 | −6.60 | −1.08 | 2.02 | −9.70 | 2.00 |

PEP-01-19-18-04 | 435.53 | −5.83 | -2.45 | −1.49 | −6.79 | 49.62 |

PEP-18-19-15-04 | 534.66 | −5.78 | −6.88 | −2.56 | −10.10 | 1.29 |

PEP-17-03-14-10 | 405.50 | −7.71 | −1.01 | 2.73 | −11.45 | 0.29 |

PEP-04-07-19-14 | 446.62 | −7.68 | 4.89 | 1.27 | −4.07 | 1009.94 |

PEP-17-09-19-15 | 506.61 | −12.07 | 11.41 | 2.83 | −3.49 | 1906.57 |

PEP-04-06-05-17 | 420.62 | −5.31 | −2.99 | 0.55 | −8.85 | 5.13 |

PEP-05-03-18-18 | 454.57 | −1.58 | −0.74 | 0.57 | −2.90 | 3676.95 |

PEP-14-14-14-18 | 463.63 | −9.46 | −2.40 | 0.91 | −12.76 | 0.07 |

PEP-02-15-03-19 | 428.54 | −3.28 | −2.99 | 1.78 | −8.05 | 12.35 |

PEP-03-08-15-19 | 444.54 | −2.26 | −5.00 | −0.81 | −6.45 | 72.74 |

PEP-08-15-17-19 | 492.58 | −9.89 | −0.26 | 0.54 | −10.69 | 0.67 |

PEP-08-15-18-19 | 508.58 | −12.30 | 0.84 | 0.38 | −11.83 | 0.19 |

PEP-09-18-18-19 | 529.60 | −7.61 | −0.28 | −0.19 | −7.70 | 18.29 |

PEP-10-18-18-19 | 543.58 | −10.16 | −0.81 | 0.19 | −11.15 | 0.40 |

PEP-13-06-04-19 | 474.63 | −10.05 | −1.60 | 0.76 | −12.42 | 0.10 |

^{[a]}Designed analogues;

^{[b]}M

_{W}represents molecular mass of the inhibitor;

^{[c]}$\u2206\u2206{\mathrm{H}}_{\mathrm{MM}}$ represents the relative enthalpic contribution to the Gibbs free energy change related to the FP3-PEP complex formation $\u2206\u2206{\mathrm{G}}_{\mathrm{com}}$;

^{[d]}$\u2206\u2206{\mathrm{G}}_{\mathrm{sol}}$ represents the relative solvation Gibbs free energy contribution to $\u2206\u2206{\mathrm{G}}_{\mathrm{com}}$;

^{[e]}$\u2206\u2206{\mathrm{TS}}_{\mathrm{vib}}$ represents the relative entropic (vibrational) contribution to $\u2206\u2206{\mathrm{G}}_{\mathrm{com}}$;

^{[f]}$\u2206\u2206{\mathrm{G}}_{\mathrm{com}}$ represents the relative Gibbs free energy change related to the enzyme-inhibitor FP3-PEP complex formation (see Equation (9));

^{[g]}${\mathrm{IC}}_{50}^{\mathrm{pre}}$ represents the predicted inhibition constant towards PfFP3 calculated from $\u2206\u2206{\mathrm{G}}_{\mathrm{com}}$ using correlation (Table 3).

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**MDPI and ACS Style**

Bekono, B.D.; Esmel, A.E.; Dali, B.; Ntie-Kang, F.; Keita, M.; Owono, L.C.O.; Megnassan, E. Computer-Aided Design of Peptidomimetic Inhibitors of Falcipain-3: QSAR and Pharmacophore Models. *Sci. Pharm.* **2021**, *89*, 44.
https://doi.org/10.3390/scipharm89040044

**AMA Style**

Bekono BD, Esmel AE, Dali B, Ntie-Kang F, Keita M, Owono LCO, Megnassan E. Computer-Aided Design of Peptidomimetic Inhibitors of Falcipain-3: QSAR and Pharmacophore Models. *Scientia Pharmaceutica*. 2021; 89(4):44.
https://doi.org/10.3390/scipharm89040044

**Chicago/Turabian Style**

Bekono, Boris D., Akori E. Esmel, Brice Dali, Fidele Ntie-Kang, Melalie Keita, Luc C. O. Owono, and Eugene Megnassan. 2021. "Computer-Aided Design of Peptidomimetic Inhibitors of Falcipain-3: QSAR and Pharmacophore Models" *Scientia Pharmaceutica* 89, no. 4: 44.
https://doi.org/10.3390/scipharm89040044