UNIVERSIDADE FEDERAL DO PIAUÍ

CENTRO DE CIÊNCIAS DA NATUREZA

PROGRAMA DE PÓS-GRADUAÇÃO EM QUÍMICA

"Potential of Peptides Derived from Laminin-1 as a

Strategy for the Regulation of Integrins during Cell
Adhesion Processes"

Doutorando: Francisco da Chagas Pereira de Andrade

Orientador: Prof. Dr. Anderson Nogueira Mendes
 PRESENTATION

Msc. Francisco das Chagas P. de Andrade

Prof. Dr. Anderson Nogueira Mendes

2
 INTEGRINS

Figure 1. Integrins can bind to a diverse range of ligands, which can be broadly categorized into: RGD
receptors, laminin receptors, leukocyte-specific receptors, and collagen receptors.
Source: https://www.mechanobio.info

3
 INTEGRINS

Lamini-1

Low-affinit
α
β
α
Active
Inactive
β

αβ
Integrin α6β1
Extended closed

Extended Open
Bent
Cell
Figure 2. The structure of integrin. The conformational changes from bent-closed, to extended-
closed, and finally to extended-open state. By Authors.
4
LAMININ-1

5
 RESEARCH OBJECTIVES
• Analyze the structure of Laminin-1 peptides and identify their molecular, physicochemical,
pharmacokinetic and pharmacodynamic characteristics of peptides derived from Laminin-1, including
their sequences and three-dimensional structures.

• Investigate the interactions between peptides and α1β3 and α1β6 integrins through molecular docking
simulations, seeking to identify the most promising binding sites.

• Explore, through molecular dynamics simulations, the interactions between Laminin-1 peptides and
integrins, α1β3 and α1β6; observing conformational changes and dynamic behaviors over time.

• Evaluate the stability of peptide-integrin complexes through molecular dynamics simulations, assessing
the strength and nature of interactions over time, and identify residues in integrins affected by
interactions, relevant to modulation

• Evaluate the stability, as well as the thermodynamic properties of peptide-integrin complexes, and
investigate how Laminin-1 peptides can influence the conformational states of integrins.

• Contribute to the development of future therapeutic strategies based on the regulation of integrins by
peptides derived from Laminin-1, supporting the rational design of bioactive compounds for the
treatment of inflammatory diseases and cancer. 6
 METHODS

Gaussian.com iqmol.org

https://avogadro.cc/ 7
METHODS

preadmet.bmdrc.kr/

admetmesh.scbdd.com/

lmmd.ecust.edu.cn/admetsar2

tox-new.charite.de/protox_II/
8
 METHODS

Table 1. Resolution PBD structure

Macromolecule Code Method Resolution
X-RAY
7ceb 2.89 Å
DIFFRACTION
Integrin α6β1
X-RAY
7cea 2.55 Å
DIFFRACTION
Integrin α3β1 P26006 ALPHAFOLDER -

www.rcsb.org https://www.uniprot.org/

9
 METHODS

rbvi.ucsf.edu/chimera/ 3dsbiovia.com pymol.org

wenmr.science.uu.nl/haddock2.4/ vina.scripps.edu/ dockthor.lncc.br/v2/

10
METHODS

11
 RESULTS
Table 2. Physicochemical property of IKVAV peptide.
Property ADMETSAR ADMETlab 2.0 ProTox II
Molecular Weight (MW) 528.70 528.36 528.58
Num. heavy atoms Up up up
Fraction Csp3 Up 0.8 up
Volume Up 546.496 up
Density Up 0.967 up
nHA (Acceptor ) 7 12 16
nHD (Donor ) 7 9 11
nRot 17 21 23
nRing up 0 up
Molar Refractivity up up 150.86
MaxRing up 0 up
nHet up 12 up
fChar up 0 up
nRig up 5 up
Flexibility up 4.2 up
Stereo Centers up 6 up
TPSA (Ų ) up 205.74 284.25
18.85
Pure water solubility (g/L) up up
Buffer_solubility_(g/L) up up 1.483
Log S (mol/L ) -1.889 -1.994 -1.552
Log P up -0.08 0.918
Log D up -0.368 -3.762
12
 RESULTS
Table 3. Absorption of IKVAV peptide.

Property ADMETSAR ADMETlab 2.0 PreADMET

Skin_Permeability up up -3.756
Caco-2 Permeability (nm/s) up -6.791 20.79
MDCK Permeability (nm/s) up 0.00011 0.136
Pgp-inhibitor Yes Yes No
Pgp-substrate Yes Yes up
HIA 0.77 0.914 12.65
F20% up 0.95 up
F30% up 0.20 up

13
 RESULTS

Table 4. Distribution of IKVAV peptide.

ADMETS PreADME
Property ADMETlab 2.0
AR T
PPB (Plasma Protein Binding) (%) 0.271 8.131 23.164
Fu (Fraction unbound in plasms) up 70.68 up
VD (Volume Distribution) (L/kg) up 0.577 up
BBB (Blood–Brain Barrier) (%) 0.67 0.068 0.036

14
 RESULTS
Table 5. Metabolism of IKVAV peptide.

ADMETS
Property ADMETlab 2.0 PreADMET
AR
CYP1A2 inhibitor No No up
CYP1A2 substrate up No up
CYP2C19 inhibitor No No No
CYP2C19 substrate up No up
CYP2C9 inhibitor No No No
CYP2C9 substrate Yes No up
CYP2D6 inhibitor No No No
CYP2D6 substrate No No Weakly
CYP3A4 inhibitor No No Inhibitor
CYP3A4 substrate Yes No Weakly

15
 RESULTS

Table 6. Excretion of IKVAV peptide.

ADMETlab
Property ADMETSAR PreADMET
2.0
CL 3.817
up up
(Clearance Rate) mL/min/kg
T1/2
up 0.81 h up
(Half Life Time)

16
 RESULTS

Table 7. Toxicity of IKVAV peptide.

ADMETla ADMETl
Property ADMETSAR b PreADMET Property ADMETSAR ab PreADMET
2.0 2.0
hERG Blockers up Inavtive Ambiguous Acute Oral Toxicity III up up
H-HT (Human Hepatotoxicity) up Low-risk up Acute algae toxicity up up 0.00877
DILI (Drug Induced Liver Injury) up No-risk up NR-AR up Active up
AMES Toxicity Non-mutagen Negative Mutagen NR-AR-LBD up Inactive up
Rat Oral Acute Toxicity (mol/kg) 3.347 Non-toxity up NR-AhR up Inactive up
Non- NR-Aromatase up Inactive up
Skin Sensitization Negative up NR-ER up Inactive up
sensitizer
Non- NR-ER-LBD up Inactive up
Eye Corrosion Negative up NR-PPAR-gamma up Active up
corrosive
Non- SR-ARE up Inactive up
Eye Irritation Negative up SR-ATAD5 up Inactive up
irritant
Respiratory Toxicity Positive Toxicant up SR-HSE up Inactive up
FDAMDD (Maximum Recommended SR-MMP up Inactive up
up Negative up SR-p53 up Inactive up
Daily Dose)
Carcinogencity Negative up up Acute Toxicity Rule up No alerts up
Carcinogenicity (Mouse ) up up Negative Genotoxic Carcinogenicity Rule up No alerts up
Carcinogenicity (Rat ) up up Negative NonGenotoxic Carcinogenicity Rule up No alerts up
Bioconcentration Factors up 0.348 up Skin Sensitization Rule up Two alerts up
IGC50 (Tetrahymena pyriformis) 0.34 3.064 up Aquatic Toxicity Rule up No alerts up
LC50FM (Acute Fathead Minnow) up 3.711 0.4847 NonBiodegradable Rule up No alerts up
LC50DM (Acute daphina toxicity ) up 4.328 0.9378 SureChEMBL Rule up No alerts up
LC50MM (Acute medaka toxicity) up up 1.4701

17
 RESULTS
Table 8. Interaction Types and Amino Acids involved in the interaction of integrin α3β1 (PDB ID:
3VI3), integrin α5β1 (Uniprot ID: P26006), integrin α6β1 (PDB ID: 7CEB) with IKVAV.
Pi -Alkyl/
Bond Pi -Aryl
Hydrogen Hydro- Carbon
Length (Å) Attractive
Name Bond (HB) phobic Hydrogen Pi -Pi
for HB Charge
interaction interaction Bond T-Shaped
interaction
interaction
Gln146 (A) 2.71 His181 (A) Glu183 (A) Leu148 (A) Asp113 (A)
Gln146 (A) 2.87 Cys185 (A) His116 (A)
Integrin
Gln146 (A) 3.14 Asn186 (A)
α3β1
Lys161 (A) 2.77
Ser187 (A) 2.78
Glu124 (A) 2.73 Glu81 (A) Tyr208 (A) Glu124 (A)
Integrin Glu124 (A) 2.73 Thr123 (A) Ile210 (A) Asp154 (A)
α5β1 Glu124 (A) 2.80 Leu209 (A)
Lys 125 (A) 2.75
Arg155 (A) 2.72 Leu156 (A) Glu215 (A) Glu219 (A)
Tyr188 (A) 3.10 Lys161 (A) His277 (A)
Integrin
Glu215 (A) 3.32 Phe162 (A)
α6β1
Gly217 (A) 2.96 Ile196 (A)
Gly218 (A) 2.75 Val216 (A)

18
 RESULTS

Table 9. Integrins docking pocket site binding energy in complex white IKVAV obtained from
HADDOCK.

Evdw Eelec Edesol EAIR

Protein HADDOCK
score RMSD BSA
(Å2) Z-score
(kcal mol-1) (kcal mol-1) (kcal mol-1) (kcal mol-1)

integrin
-43.4 0.2 -28.7 -64.6 -6.5 46.9 688.0 -1.8
α3β1

integrin
-48.4 0.6 -16.5 -119.4 -8.0 0.4 669.6 -1.5
α5β1

integrin
-44.6 0.4 -22.5 -119.2 0.4 12.7 688.7 -1.9
α6β1

19
 RESULTS

A B

Figure 3. Molecular Structure of peptide IKVAV. A- 2D Molecular Structure. B- 3D Molecular Structure. 2D structure were building in
the tool draw peptide primary structure PepDraw (https://pepdraw.com/). 3D structures were drawn in Avogrado and saved by SAMSON 22 R.
The structures were optimised using IQMol software, version 2.11.1 (http://iqmol.org/).

20
 RESULTS

A B A B
Laminin-111
Integrin α3β1

C
C

integrin
α6β1
Laminin-111

Figure 4.1. Laminin-111 docking and molecular interaction with integrin
α3β1. (A) Laminin-111 alignment with integrin α3β1 cartoon; (B)
hydrophobic molecular interaction of Laminin with integrin α3β1; (C)
hydrophobic molecular interaction of Laminin with integrin α3β1surface; The
dashed lines in yellow evidence the hydrophobic interactions.
Figure 4.2. Laminin-111 docking and molecular interaction with
integrin α6β1. (A) Laminin-111 alignment with integrin α6β1 cartoon;
(B) hydrophobic molecular interaction of Laminin with integrin α3β1; (C)
hydrophobic molecular interaction of Laminin with integrin α3β1surface;
The dashed lines in yellow evidence hydrogen bond interactions.

21
 RESULTS
A YIGSR B

Figure 5. IKVAV molecular docking and molecular interaction with integrin α3β1. (A) IKVAV alignment with integrin α3β1 hydrophobic
pocket; (B) molecular interaction of IKVAV with integrin α3β1 hydrophobic binding pocket; (C) IKVAV alignment with binding pocket of the
integrin α3β1 with coordinated active fragments His 116, Gln 146, Lys 161, His 181, Glu 183, CYS 185, Ser 187;
22
 RESULTS
A B

YIGSR

Figure 6. YIGSR molecular docking and molecular interaction with integrin α6β1. (A) YIGSR alignment with integrin α6β1 hydrophobic
pocket; (B) molecular interaction of YIGSR with integrin α6β1 hydrophobic binding pocket; (C) YIGSR alignment with binding pocket of the
integrin α6β1 with coordinated to active fragments Arg 155, Leu 156, Lys 161, Tyr 188, Glu 215, Val 216, Gly 217, Gly 218, Glu 219, His 277.
23
 RESULTS

Figure 7: HADDOCS score versus i-RSMD. A) YIGSR interactions with integrin α3β1; B) YIGSR interactions with integrin α5β1;
D) Clusters integrin α6β1@Laminin-111.

24
 RESULTS

A Protein Complex B Protein Complex

Figure 8: Ramachandran plot. (A) YIGSR -Integrin α3β1 complex; (B) YIGSR -Integrin α6β1 complex. Amino acids are represented
in green; the most favorable regions are delimited by blue lines; the more permissive additional regions are delimited by magenta lines;
and non-permissive regions correspond to unbounded regions. Graphs were generated in Software Discovery Studio 2020.

25
 NEXT STEPS IN DATA ANALYSIS

• Molecular Dynamics

1- Molecular Dynamics: Carry out simulations to observe the dynamics of

interactions over time.

2- Stability of Complexes: Evaluate the stability of peptide-integrin complexes

through molecular dynamics simulations.

3- Inhibition Mechanisms: Identify by simulations the key residues in integrins

that may be promising targets for the modulation cell adhesion processes.

4- Experimental Validation: Compare results with Molecular Docking data.

26
Thank You!

27