Pengembangan Molekul Baru sebagai Kandidat Obat Covid-19 Prof. Dr. apt. Siswandono, M.S. POM CNC BSUS Meehan h wer enc ment y Webinar FF Unair, Surabaya 3 Agustus 2020MEDICINAL CHEMISTRY PATIENTS t GED PHARMACISTS Identification of lead compounds insilico screening 1 \ wv + PK/PO ADME = Clinical test Approval ares — sToxity ——=> __Phasetest. => - Marketing authorisation + Formulation Chemical synthesis, “Moan mn enwannn Screening (HTS, in vivo, etc), Lead optimisation J J } PROCESS CHEMISTRY Cost (reagent, catalysts, solvent, etc], reaction steps, purification, Breen chemistry klo- to ton-scale, safety, polymorphism, stability, GMP, etc The International Pharmaceutical Federation (FIP), 2018Paradigma Baru dalam Drug Discovery & Development eT AR ered Find a drug effective against disease protein Isolate protein (2-5 years) involved in 5 Scale-up disease (2-5 years) Human clinical trials (2-10 years) ' BS oy! Formulation ay ' e IND : Investigational New Drug FDA approval NDA: New Drug Approval (2-3 years) Preclinical testing | (1-3 years)TEKNOLOGI YANG TERLIBAT Pec eae ce Cea GENOMICS & PROTEOMICS wporet ts and “personalize HIGH THROUGHPUT SCREENING Screening up to 100,000 compounds a day for activity against a target protein &, — VIRTUAL SCREENING Using a computer to predict activity COMBINATORIAL CHEMISTRY Rapidly producing vast numbers of compounds MOLECULAR MODELING Computer graphics & models help improve activity IN SILICO & IN VITRO ADME MODELS Computer & Tissue models begin to replace animal testing ical testingVv wy PENGEMBANGAN OBAT 3) Memilih sasaran penyakit dan target obat (reseptor) Skrining senyawa dari bahan alam/hasil sintesis yang mempunyai efek biologis dan menentukan senyawa induk (lead compound) Tsolasi dan pemurnian senyawa induk Menentukan struktur senyawa induk Identifikasi hubungan struktur-aktivitas (SARs) dan farmakofor senyawa Studi in silico senyawa induk dan turunannya Sintesis senyawa induk dan turunannya Rancangan Obat yang Rasional (Rational Drug Design). Studi preklinik lanjut Studi Hubungan Kuantitatif Struktur-Aktivitas Pengembangan formulasi Uji klinik (Fasa I s.d. III) Persetujuan ijin edar oleh yang berwenang (BPOM, FDA dll.)Memilih sasaran penyakit dan target obat = Sasaran penyakit: Covid-19 (SARS-CoV-.)tesis Cocid- Ig ae-tec) SARS-CoV2 8. Virion release Cytoplasm S-Protein. Cell 1, SARS-CoV2 Entry a! gon E-Protein. if mS)» uembrane Fusion =f 3 gate is } Pas & x 3. RNA release ¢ 4. Translation & 3 = ? 3 — #3 2: - % é = 2s gg i “ E Z ge 2 as t ae 6. Translational & 5 Viral RNA’ Polypeptide evenenveee 5. RNA replication | [ -Ab Endocytosis ont gy Target Obat (Reseptor/Enzim) e Sy / ra re.Isolasi protein (reseptor/enzim) Dea aca) ae Ns aU) Peel = ‘mass. Comparing them reveals 2 protein (circted] overproduced by Covid-I9 Cae ata) tea Pretend pees’ reer Rote peeCovid-19 Receptors and PDB ID Oa UOC CRUCIBLE OM WAS era Re CL) The crystal structure of COVID-19 main protease in complex with an inhibitor N3 (6LU7) ORCL Ce Re OATES U to CoV-2 by remdesivir fosfat (7BV2) Nee Cs hee OME RS Cm Corte eCA CAD) SO TORU RO ea Re Sane LC Ker By Structure of the SARS-CoV-2 spike glycoprotein (closed state) (6VXX) SCOR UR OO) OO eNO cue Ren Cm ORT OSE eer ant antibody Fab fragment (state 2) (6XCN) COMO S a UL OOS eee nee RCT mM Tots PNT SON YIN) Crystal structure of SARS-CoV-2 (Covid-19) NSP3 macrodomain in complex with MES (6YWM)Covid-19 Receptor, PDB ID: 7BV2 RNA-dependent RNA polymerase PiU SyL to ON E77Covid-19 Receptor, PDB ID: 5R84 SARS-CoV-2 main proteaseSkreening molekul eS) Melalui CADD (Computer Assisted Drug Design): The use of CADD approaches can reduced the cost of ColaUremeroen comme Tiel AT Coley ritalin ce) 50% (Xiang et al., 2012)S353 DDB) (Structure Based Drug Design) Design & synthesis of new Bid) (Ligand Based Drug Design) LLoanecesor eorex Surabhi & Singh (2018)Structure-Based Drug Design SARS-CoV-2 main protease, PDB ID: 5R84 Pe Cea g ete ed Rena) Eman Cer Ee Cer ea DE ae era utes! eens!Pub@hem wo 9 ss wo Ligand-Based Drug Design COVID-19 VIRUS Q 35 2 text search, Lean more about COVID-19 (Coronavirus Disease 2019) data in PubChem. & erch in Entn a UNIL-3QKI37EEHE; Remdesivirum; Remdesivir[USANI; Remdesivir, 1809249-37-3; MW: 100-600; Torsion: max 14; H Bond Donor: max 10; H Bond Acceptor: Polar Area: 10-150; XLogP: -5 s/d +6 Filter: gugus farmakofor 4 senyawa > DocCompound Screening in Plant re) MU itom rier MOEN Ce nile eh wiiceme stl (ere om TENET RNC Flavanones: pinostrobin (compound PTT co FOL CeLeccrT Oa CTT pam aC MUO eae) LUCE SE Len Le LCela LL and 7.4’-dihydroxy-5-methoxyflavanone [eg aU P Zeno (Chahyadi et al., 2014; Nguyen et al., 2017). Boesenbergia pandurata Roxb. Schlecht PUMICE osha T CROs | AVS cocci SIRO ENLOUUB SB ACLU TUOMS ent oat mey ONL Coe PASS Cec) M (Eng-Chong et al., 2012) From n-hexane extract of rhizome: Pinostrobin (1-2%) Patel et al., 2015: Pinostrobin inhibits herpes simplex virus-1 (HSV-1) replication, and inhibit 88.7% of dengue-2 virus NS3 protease > potential compound to developted for anti Covid-19.beiitesteeity PRontod erage ones t oni eSeaelehtad R =alkil (C,H),,,), alkil halida, sikloalkil dsb.nya ESI MB COHUMCORI TOOLS Ome tu (Clem pTulerU MCR eItLS Menlo m Ini) Pemilihan senyawa yang akan disintesis harus Sion eoueen ee Ce CROCE MOEN Stree yang ada di pasaran.Aktivitas biologis dipengaruhi oleh sifat-sifat kimia fisika: 1. Sifat lipofilik/hidrofobik > mempengaruhi kemampuan senyawa dalam menembus membran biologis (distribusi obat ke reseptor), . Sifat elektronik > mempengaruhi kekuatan ikatan obat- reseptor dan kemampuan senyawa dalam menembus membran biologis (bentuk molekul obat), RAST Cul aie MOON CM NSE TSEU BTN COE LOS etree Coo) Sifat kimia fisika yang berhubungan aktivitas obat: kelarutan, koefisien partisi, adsorpsi, aktivitas permukaan, derajat ionisasi, isosterisme, ikatan kimia (kovalen, ionik, hidrogen, dipol-dipol, van der Waals dan hidrofobik), jarak antar atom, dan konfigurasi molekul dalam ruang (isomer).SMELLS CACB Tt as clemarasrecleraye| 1. Memprediksi sifat kimia fisika Lipofilik: 7, logP, ClogP, tPSA, solubility, dll., Elektronik: 6, pKa, E,,., Eyomo» Eyemo> dll., Sterik: Es, BM, MR, CMR, B,-B;, Vol. VdW, dll. . Memprediksi sifat biologis Absorpsi/Bioavailabilitas, Distribusi, Metabolisme, Ekskresi, Toksisitas (LD, rat, hepatotoksik, sens itas kulit dll.), Karsinogenik, Drug-likeness. . Memprediksi aktivitas biologis (Proses interaksi Obat- Reseptor = Docking) Dock Score, Mol Dock Score, Rerank Score dll.Program Komputer untuk Studi In Silico 1. Memprediksi sifat kimia fisika ChemDraw, Maestro, Discovery Studio, MOE, SYBYL QSARToolbox, ACD/I-Lab etc. . Memprediksi sifat biologis QSARToolbox, ACD/I-Lab, Osiris Property Explorer, pkCSM, ProToxII, PreADMET, SWISSAdme, PAS, MOE, Maestro, Discovery Studio, SYBYL, etc. RPC celh meee ORO sy Argus Lab, Autodock/Vina, MolegroVirtual Docker, SWISS Model, Lead It, Discovery Studio, MOE, Maestro, SYBYL, Plants, DOCK, GROMAG, AMBER, DRAGON, etc.CONTOH PREDIKSI ADMET by pKCSM online tool Poin Te eae) 2. Skin permeability RO ae et“ 0 Re ae 1. Steady State of Volume Distribution (human) Pe eleM Eom LLL ONL SoC cly ae ry coe BONS cece a PAP RN ord Pa Peer ie PEO oC A RGR tt) OY lace a yea) Kee CO. lai Oe) Ga a eee eee |e 3. Ames toxicity (carcinogenic)Lipinski Rule of Five A candidate molecule is more likely to have poor PLO w OM outta 1. The molecular weight exceeds 500. 2. The calculated octanol/water partition coefficient (ClogP) exceeds 5. 3. There are more than 5 H-bond donors expressed as the sum of O-H and N-H groups. 4. There are more than 10 H-bond acceptors expressed as the sum of N and O atoms.‘Mohammad ikl adh Pratama'/ Had Peerwono!/Siswandono Sswodiharjo! ADMET properties of novel 5-O-benzoyl| derivatives inostrobin Design and molecular docking of novel 5-O-Benzoylpinostrobin derivatives as anti-breast cancer Mohammad Rizki Fadhil Pratama', Hadi Poerwono", 8. Siswandono” M1 Gmail Molecular Docking of Novel 5-O- benzoylpinostrobin Derivatives as SARS- CoV-2 Main Protease Inhibitors = for publication in Loa Pharmaceutical Sciences, Please nate that you wll be able to make any necessary corrections to your paper when you receive the production ‘The production proofs willbe emailed to you within the next few submitting your fine paper to Pharmaceutical ing adeitonal papers from you nthe Ali shayanfar (Pharm.D, PhO: ate Edtor Scopus) Beormvve+ i+arom ty oS Saye SSS Acyclovir -82,6489 82,1625 -82,2254 —-82,3456 Remdesivir -95,4316 -94,7320 —-95,0633—-95,0756 Favipiravir -64,3003 -63,9869 -63,9556 ~64,0809 Oseltamivir -94,2573 95,0396 -93,4564——-94,2511 Chloroquine -86,4063 87,3212 -85,9418 —-86,5564 Hydroxychloroquine -87,1314 -86,6264 —-87,7532_—--87,1703 Pinostrobin 87,4432 -87,8617 -87,4859 -87,5969 5-O-(Acetyl)pinostrobin -109,8390 — -109,8350 -109,0580 —-109,5770 5-O-(n-Hexanoy!)pinostrobin -103,7010 — -103,8350 -102,9680 —-103,5010 -O-(Benzoyl)pinostrobin -103,9270 -103,5370 -103,5180 — -103,6610 5-O-(4-t-Butylbenzoy!)pinostrobin -112,0070 -112,1830 -112,1700-112,1200 Andrographolide 99,9285, -99,1510 -99,1018 -99,3938 Ligand 5R84 -82,9324 82,8657 -82,3303-—-82,7095 By Molegro Virtual Docker 5.5Hasil Docking (Interaksi Obat-Reseptor) Pinostrobin lo} = ie for) am Ligand 5R84 cx} EReng Coon Titers fone) aw (c=x3) a PronCnt ocion ls Pecos 5-O-(4-t-Butylbenzoyl)pinostrobin oxyHasil Docking = Senyawa uji mempunyai nilai Rerank Score lebih abi dibanding senyawa pembanding > ikatan obat-reseptor lebih stabil > diprediksi tahwa senyawa ji, by in silico, mempunyai aktivitas yang lebih tinggi dibanding senyawa pembanding. sa Senyawa layak untuk disintesis dan dikembangkan lebih lanjut sebagai calon obatSintesis senyawa induk dan turunannya Melakukan sintesis sejumlah turunan senyawa induk, dan konfirmasi struktur senyawa hasil sintesis (Kimia Sintesis, Kimia Kombinatorial) Gugus atau substituen yang disubstitusikan dipilih dengan menggunakan: metode Topliss, metode pencarian Fibonacci, metode rangkaian optimisasi simpleks atau analisis klaster.Sintesis 5-O-acyl/benzoylpinostrobin CSM ee Co) Metoda Sintesis: Esterifikasi > Reaksi Scotten-Bouwmann. OF Te Ccaaelaa icra aad @ ltamel1a KLT. Konfirmasi Struktur: FTIR, NMR (C dan H) and Spektrometer Massa.Uji Pre-klinik Lanjut Uji aktivitas in vitro dan in vivo Formulasi skala lab > kilo Studi ADME & toksisitas Studi Hubungan Struktur-Aktivitas (Kualitatif dan Kuantitatif)QSAR (Quantitative Structure-Activity OE Latey eer os) Compounds + biological activity Statistic na ) Descriptors: ni Lipophilic Electronic Steric INCOVAC HY UTCCMUY COMTI RON Kee biological activityQSAR ® © De Novo: Free-Wilson Approach © 2-D/3-D QSAR: Hansch method © Original idea: LFER (Hammet equations). e Attempts to identify and quantitate physicochemical properties of a drug (descriptors) in relation to its biological activity or binding. ¢ Studies lipophilic (i.e. 2, logP, ClogP, tPSA), electronic (i.e. 6, pKa, Exot Enomor Etemo), and steric (i.e. Es, MW, MR, CMR) properties, either whole molecule or pieces/part/group. © Statistical Program: Coa |e BsdeasoPmsy cole yele PSV Cee] ToL (IRL eT ola et TeM gta SK 1mKesimpulan & Harapan ® 1. Studi Molecular Modeling (Uji in silico) telah banyak digunakan dalam upaya pengembangan obat baru, dan dapat menurunkan pembiayaan sebelum uji klinik sampai + 50%. . Senyawa bahan alam Indonesia, seperti Pinostrobin yang berasal dari temu kunci sangat menjanjikan untuk dikembangkan lebih lanjut sebagai obat Covid-19. . Mengingat bahwa sudah ada obat dan vaksin Covid-19 dalam proses uji klinik fase III, diharapkan pada tahun 2021 obat dan vaksin tersebut sudah tersedia di pasaran.a cise Valetet) Bete eae Ogee eRe oe Pmt Ce) nieve eRe nine on aars ien ne ew Hirano, T. & Murakami, M., 2020. COVID-19: A New Virus, but a Familiar Receptor and Cytokine Release Syndrome, Immunity, 52 (5), 731-733. Magrone, T., Magrone, M., & Jitillo, E., 2020. Focus on Receptors for Coronaviruses with Special Reference to Angiotensin-converting Enzyme 2 as a Potential Drug Target -A Perspective. Endocrine, Metabolic & Immune eee Re Mehta, S.S., 2008. Typical Drug Development Process, hio:|\www-globalspec.com reference/57697/203279/4-8- typical-drug-development-process. Rut, W., Zmudzinski, M., Lyu, Z., et al, 2020. Activity profiling and structures of inhibitor-bound SARS-CoV-2- PLpro protease provides a framework for anti-COVID-19 drug design, bioRxiv, 1-18. ee eon en MEU ean eed Siswandono, 2014. Pengembangan Obat Baru, Surabaya: Airlangga University Press. Siswandono (Ed), 2016. Kimia Medisinal I, Edisi Ke-2, Surabaya: Airkangga University Press. Surabhi & Singh, B.K., 2018. Computer Aided Drug Design: An Overview. Journal of Drug Delivery & Dee Od van Tonder, J.J., Steenkamp, V. and Gulumian, M., 2013, Pre-Clinical Assessment of the Potential Intrinsic Hepatotoxicity of Candidate Drugs, in Gowder S, ed., New Insights into Toxicity and Drug Testing. ). WHO: Scientific brief, COVID-19 and the use of angiotensin-converting enzyme inhibitors and receptor blockers, Uy Aras UMM I QUAY ATMA =r Sees ee Meee eeN tee LO eA SU ems CenTerima kasih Eye) Perhatian Anda i. 7