9th_Advanced_in_Silico_Drug_Design_Workshop_2026_Martinat_D_Berka_K_Polischuk_P by Flexibooks

Book of Abstracts

This publication was created with the support of ELIXIR-CZ (LM2023055), EATRIS-CZ (LM2023053), and CZ-OPENSCREEN (LM2023052) infrastructures

This work is licensed under a Creative Commons BY license (Attribution) The license terms can be found at https://creativecommons org/licenses/by/4 0/

Managing editor Otakar Loutocký

Proofreading Karel Berka, Pavlo Polischuk

Graphic design Dominik Martinát, Nina Kadášová, Anna Špačková

Typeset by Dominik Martinát

Published by Palacký University Olomouc, Křížkovského 8, 779 00 Olomouc vydavatelstvi.upol.cz vupshop.cz vup@upol cz

VUP 2026/0026

Not for sale

1st edition

Editors © Dominik Martinát, Karel Berka, Pavlo Polischuk, 2026

https://doi.org/10.5507/prf.26.24467399

ISBN 978-80-244-6739-9 (online: iPDF)

9ADD workshop (2612026 – 3012026) is focused on using in silico tools and approaches in drug design. Wecoverbothstructure-baseddrugdesign(moleculardocking,moleculardynamics,structural bioinformatics tools) and ligand-based drug design (QSAR, pharmacophores, deep learning) with lecturesandon-handtutorials.

WelcometoOlomouc!

KarelBerkaandPavloPolishchuk

InvitedLecturers

● ThierryLanger(UniVie,Vienna)

● AlexandreVarnek(UniStrasbourg)

● HanochSenderowicz(Bar-IlanUniversity)

● JohannesKirchmair(UniVie,Vienna)

● SemenYesylevskyy(IOCBPrague,KFCUPOL,Receptor.AI)

● FedericaMoraca(UNINA,Napoli)

● WimDehaen(UCTPrague)

● MartinŠícho(UCTPrague)

● MartinLepšík(IOCBPrague)

● AleixGimenoVives(URV,Tarragona)

● PeterErtl(ErtlMolecular)

● CorinWagen(RowanSci)

● JonathonVandezande(RowanSci)

● MarianNovotný(CharlesUPrague)

● NiklasPietDoering(FreieUniversitätBerlin)

● ValerijTalagayev(FreieUniversitätBerlin)

● MarkoJukic(UMaribor)

● PodlipnikČrtomir(ULjubljana)

● IgorTetko(HMGU)

● KarelBerka(KFCUPOL)

LocalOrganizers

● PavelPolishchuk(IMTMUPOL)

● GuzelMinibaeva(IMTMUPOL)

● AleksandraIvanova(IMTMUPOL)

● VáclavBazgier(KFCUPOL)

● KateřinaStorchmannová(KFCUPOL)

● DominikMartinát(KFCUPOL)

● AnnaŠpačková(KFCUPOL)

● JindřichLněnička(KFCUPOL)

● ElizabethKolářová(KFCUPOL)

● JanSalomon(KFCUPOL)

● PetrStadlbauer(KFCUPOL)

Venue

FacultyofScience,PalackyUniversityOlomouc,CzechRepublic tř.17.listopadu12,Olomouc GPS:49.5924922,17.2632337

3rd floorPCroom3.002+lectureroom2.001

ListofOn-SiteParticipants

1. AbonyiStanleyArinze,UniversityofNigeria,Nsukka,NG

2. ÁdámLévárdi-ComeniusUniversityBratislava,SK

3. AlessandroFabiano,UniversitàDegliStudiDiNapoliFedericoII,IT

4. AmirMahdiZardoshti-SharifUniversityofTechnology,Tehran,IR

5. AndreaBarboraVaňková-UniversityofChemistryandTechnology,Prague,CZ

6. AnnaŠpačková-PalackyUniversityOlomouc,CZ

7. AntonellaPiaIuliano,UniversitàDegliStudiDiNapoliFedericoII,IT

8. AnubhaKumari-VinobaBhaveUniversityHazaribagh,IN

9. AqsaIjaz-UniversitàDegliStudiDiNapoliFedericoII,IT

10.ArmandoTucci-UniversitàDegliStudiDiNapoliFedericoII,IT

11. ArtemLennoi-UniversityofStrasbourg,FR

12.AtilioReyesromero-PalackyUniversityOlomouc,CZ

13.AylaEren-IstanbulTechnicalUniversity,TR

14.BarboraČurdová-UniversityofChemistryandTechnology,Prague,CZ

15.BarboraHubálková-PalackyUniversityOlomouc,CZ

16.BorisKácal-PalackyUniversityOlomouc,CZ

17.ChudasmaKrishna-Indrashiluniversity,IN

18.DamilolaBodun-UniversiteParisCite,FR

19.DavidKopecny-PalackyUniversityOlomouc,CZ

20.DerrickAgwora-CharlesUniversity,Prague,CZ

21.DominikMartinát-PalackyUniversityOlomouc,CZ

22.Dr.SyedShakeelShah-UniversityofNarowal,PK

23.DragosHorvath-DragosHorvath,FR

24.EliasHossenTonmoy -MawlanaBhashaniScience&TechnologyUniversity,BD 25.ElizabethKolářová-PalackyUniversityOlomouc,CZ 26.EmmanouilArsenikos-UniversityofChemistryandTechnologyPrague,CZ 27.EmmanuelAmarkwei-MakPharmacyLtd.,GH

28.FahilEjaz-UniversitàDegliStudiDiNapoliFedericoII, IT 29.FatemeMaya-UniversitàDegliStudiDiNapoliFedericoII,IT 30.FauzanEjaz-UniversitàDegliStudiDiNapoliFedericoII,IT

31.FlaviaDellaCorte-UniversitàDegliStudiDiNapoliFedericoII,IT 32.GamalAbdelfattah-PalackyUniversityOlomouc CZ

33.GiadaBellofatto-UniversitàDegliStudiDiNapoliFedericoII,IT 34.GiorgiaAndreozzi,UniversitàDegliStudiDiNapoliFedericoII,IT

35.GiorgioVeneruso-UniversitàDegliStudiDiNapoliFedericoII,IT

36.GiuliaSaccone-UniversitàDegliStudiDiNapoliFedericoII,IT 37.GiuseppeAngelino-UniversitàDegliStudiDiNapoliFedericoII ,IT

38.GuzelMinibaeva–PalackyUniversityOlomouc,CZ

39.HarunaIsiyakuUmar-FederalUniversityofTechnologyAkure,NG 40.HassanKotey-UniversityforDevelopmentStudies,GH

41.IjeomaDuru-FederalUniversityofTechnologyOwerri,NG 42.ImranAli-GCUFaisalabad,PK

43.IsidoroCipolletta-UniversitàDegliStudiDiNapoliFedericoII,IT

44.IvanČmelo-UniversityofChemistryandTechnologyPrague,CZ

45.JanPerner-BiologyCentreAVČR,ČeskéBudějovice,CZ

46.JanSalomon-PalackyUniversityOlomouc,CZ

47.JaveriaShafqat-UniversityofGujrat,Pakistan,CH

48.JindrichLnenicka-PalackyUniversityOlomouc,CZ

49.JiříVlasák-UniversityofChemistryandTechnologyPrague,CZ

50.JoannaCeklarz-UniversityofChemistryandTechnologyPrague,CZ

51.JosephOseiOwusu-MakPharmacyLtd.,GH

52.KaciSebouai -NEBULA,FR

53.KadManaswiYogesh-IctBhuneshwarCampus,IN

54.KarolínaPlánková-PalackyUniversityOlomouc,CZ

55.KateřinaStorchmannová-PalackyUniversityOlomouc,CZ

56.KaveriPrasad-HokkaidoUniversity,JP

57.LamiriAsmaa-FacultedeSciencesdeTunis,TN

58.Lukáš Kerti-ComeniusUniversityBratislava,SK

59.LukášGibala -PalackyUniversityOlomouc,CZ

60.MariaBarraParisi,UniversitàDegliStudiDiNapoliFedericoII,IT

61.MariaCameliaDinu-UniversitàDegliStudiDiNapoliFedericoII,IT

62.MilanaDejaková-UniversityofChemistryandTechnologyPrague,CZ

63.MohammadSayfullah-NoakhaliScienceandTechnologyUniversity,BN

64.MohammadTaheriLedari-UniversityofTehran,IR

65.MohammedModatherTaha-AlSalamUniversityinEgypt,EG

66.NouranAhmedGaberMohamed -Heliopolis,EG

67.OndřejHajdušek-BiologyCentreAVČR,ČeskéBudějovice,CZ

68.OrianaVitale -UniversitàDegliStudiDiNapoliFedericoII,IT

69.PatrikMarek-PalackyUniversityOlomouc,CZ

70.PaulClarke-UniversityofAgder,NO

71.PavelKohout-MasarykUniversityBrno,CZ

72.RayaRoy-IndianInstituteofScienceEducationandResearch,IN

73.RiccardoFusco–PalackyUniversityOlomouc,CZ

74.RishabhKhare-RoyalCollegeofSurgeonsinIreland,IE

75.SaidTrujillodeLeón,UniversidadRoviraiVirgili,ES

76.SalemHaruna- MakPharmacyLtd.,GH

77.SamuelFanči -CharlesUniversity,Prague,CZ

78.SandeepSatapathy-GarvanInstituteofMedicalResearch,AU

79.ShamimSafaei-UniversitàDegliStudiDiNapoliFedericoII,IT

80.ShetuRoy-MawlanaBhashaniScience&TechnologyUniversity,BA

81.StanislavTricolici-PalackyUniversityOlomouc,CZ

82.Taposh-MawlanaBhashaniScience&TechnologyUniversity,BD

83.TerezaKubatova-UniversityofVienna,AT

84.Thanh-AnPham-UniversityofStrasbourg,FR

85.TieuLongPhan-ProfessurfürBioinformatik,InstitutfürInformatik,Universität Leipzig,DE

86.TomášJelínek-CharlesUniversity+BIOCEV,CZ

87.TruptiPatil-Instituteofchemicaltechnology,IN

88.TuyetMinhPhan-UniProfessurfürBioinformatik,InstitutfürInformatik,Universität Leipzig,DE

89.VaclavBazgier-PalackyUniversityOlomouc,CZ

90.ValeriiaFil-UniversityofChemistryandTechnologyPrague,CZ

91.VishmaPratapSur-IPPTPAN,Warsaw,PL

92.VítNovotný -UniversityofChemistryandTechnologyPrague,CZ

93.WiktorNisterenko-MedicalUniversityofGdansk,PL

94.YehorFranchuk-TarasShevchenkoNationalUniversityofKyiv,Instituteof MolecularBiologyandGeneticsNASUkraine,UA

PosterAbstracts

HIV-1 RT Inhibitor Design via Generative AI, Screening, and MD

Damilola Bodun

Universite Paris Cite

The era of generative AI in drug design is here, and in this study, we applied a generative AI model to design potential non-nucleoside inhibitors of HIV-1 reverse transcriptase (RT). RT converts viral RNA into DNA, facilitating viral integration into a host's genome. Inhibiting RT is therefore critical in combating HIV-1. Using the REINVENT prior model, we fine-tuned it with classified RT inhibitors (pIC50 > 8.5) from ChEMBL, generating over 6000 compounds. These compounds underwent rigorous filtering, including classification by a Message Passing Neural Network (MPNN), PAINS filtering, pharmacophore modeling, structure-based screening, MMGBSA scoring, and ADMET prediction. We identified five top-performing compounds, which demonstrated superior docking scores (≤ -13.22 kcal/mol) and binding free energies (MMGBSA dG Bind ≤ -77.48 kcal/mol) compared to the reference ligand (-8.42 kcal/mol). Further ADMET predictions and Molecular dynamics simulation at 500 ns revealed that these compounds had better drug-like properties and comparable stability at the active site compared to the reference ligand. These findings suggest that the identified compounds are promising candidates for further in vitro validation to confirm their therapeutic potential against HIV-related proteins. This study highlights the transformative role of AI-driven drug discovery in addressing HIV drug resistance.