SCRIPT FOR PRESENTATION

1. BACKGROUND

Hello and thank you so much for having me. I’m delighted to be here. What a beautiful day is that I’m so
happy to be sharing my research with all of you.

Ladies and gentlemen, we often hear that patients who are positive for COVID-19 during their quarantine
look like they are in good health, even some of them are still able to do work. This may happen if a person
does not have immunity problems and does not have comorbids (the presence of more than one disorder in
the same person).

But the thing that makes the increasing of COVID-19 mortality is the presence of various comorbids (such
as TB, heart disorder) which can cause COVID-19 patients to be in a critical condition. this can happen
because the anti-COVID drugs currently being used often have incompatibilities with TB and Heart
disorder and can cause a death.
2. TITLE

Therefore, we as students engaged in medicinal chemistry want to provide a solution to this problem,
 namely in the form of computational studies (in silico) of benzoquinoline and its derivatives as candidates
for anti-COVID-19 drugs through inhibition of the Main Protease enzyme.
3. THE COVID-19

Coronavirus disease 2019 (COVID-19) is a contagious and multi-organ disease caused by severe acute
respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. SARS-CoV-2 is mainly transmitted through
air droplets and direct contact.
In SARS-CoV-2 infected patients, the immune system responds by mobilizing inflammatory cells. If a
bacterial infection concurrent, inflammation might progresses severely and rapidly destroy lung tissue,
leads to systemic hypoxia and multi-organ failure which often fatal.
4. DRUG TARGET

SARS-CoV-2 infects cells via membrane fusion initiated by binding between its spike glycoproteins to
angiotensin-converting enzyme 2 (ACE2) protein —which is highly concentrated in the surface of the
airway epithelial cells. Once viral RNA materials are released into cell cytoplasm and being translated to
polyproteins, SARS-CoV-2 main protease Mpro2 (PDB ID: 6LU7) (also named as chymotrypsin-like
protease (3CLpro2) leads proteolytic processing by digesting the polyprotein conserved sites, starting with
the autolytic cleavage of this enzyme itself from pp1a and pp1ab. This proteolysis generates functional
 polypeptides to facilitate virus replication.

The target molecule we chose was the main protease (Mpro) which plays a role in the proteolysis stage. If
that stage is inhibited, the SARS-Cov-2 virus cannot continue its replication stage. So, the Mpro enzyme is
very potential to become a drug target.
5. CURRENT THERAPY

Currently, some of the most dominant anti-covid19 regimens used in various countries are Azythromicine,
Remdesivir, Favipiravir, and Oseltamivir. However, the side effects of these drug regimens are very
dangerous. For example: arrhythmia, hepatotoxic and long QT syndrome in our heart.

Besides that, based on molecular dynamics studies, it was stated that the structure of Mpro is not suitable
for inhibitors which have a molecular mass <500 Da. So that Favipiravir & Oseltamivir can be predicted
not to have a stable binding to Mpro.

6. CHALLENGES

Therefore, the challenge for medicinal chemists today is how to find a drug that is much better than
 current drug regimens. Which drug regimens currently have disadvantages, for example poor selectivity,
cardiotoxicity, and incompatibility with anti-TB drugs, such as Azythromicine. Current drug regimens
also have a molecular mass <500 da such as favipiravir & oseltamivir. So, we carry benzoquinoline as a
lead compound because it has been shown to inhibit the Mpro of SARS-CoV-1 protease. The structure of
Mpro-1 also has a 79.5% similarity with the Mpro-2. Thus, it is highly probable that Benzo can also
inhibit Mpro Sars-Cov-2.
7. BENZOQUINOLINE WEAKNESSES

However, benzoquinoline currently has the weakness of low solubility and lack of specific antiviral
activity. Therefore, structural modification of benzoquinoline is needed to obtain better of activity and
physicochemical properties.
8. CADD

The in silico method that we use is a structure based drug design (SBDD). This SBDD was chosen
because the condition of Covid19 whose the target were well defined.

9. RESEARCH QUESTION
10. OBJECTIVES

11. RESEARCH METHODS

12. THE STRUCTURE OF BENZOQUINOLINE AND ITS DERIVATIVES

13.
Berikut merupakan struktur hasil modifikasi senyawa benzoquinoline. Terdapat 14 senuawa turunan yang
didapatkan dari hasil modifikasi struktur dimana penambahan substituent kimia berfokus pada atom C5.
Pemilihan titik ini merupakan pilihan yang tepat karena bagian tersebut memiliki reaktivitas relative yang
tinggi sehingga mudah untuk disubstitusi. Adapun penambahan gugus fungsi didasarkan pada
karakteristik reseptor Mpro yang telah dipelajari sebelumnya.
14. 3D LIGAND-BASED PHARMACOPHORE MODELLING

The first step in computational testing is to conduct pharmacophores modeling based on the 3D ligand
structure. At this stage, the mode of interaction between benzoquinolin derivatives is compared with 100
active ligands on Mpro and expressed in the form of a fit-score value. The confounding compound is used
as one of the auxiliary parameters to eliminate the unnecessary interaction modes for ligand-receptor
 interactions.

Based on this table, all benzoquinoline compounds have a fit-score value above 50%. This shows that the
benzoquinoline derivatives have similar interactions with ligands whose activity is currently stated as the
active compound.

Langkah pertama yang dilakukan dalam pengujian komputasi adalah melakukan pemodelan farmakofor
berbasis struktur 3D ligan. Pada tahap ini, mode interaksi antara senyawa turunan benzoquinolin
dibandingkan dengan 100 ligan aktif pada Mpro dan diekspresikan dalam bentuk nilai fit-skor. Adapun
senyawa pengecoh yang dijadikan salah satu parameter pembantu guna mengeliminasi mode interaksi
yang tidak diperlukan dalam interaksi ligan dengan reseptornya.

Berdasarkan tabel ini, dapat diketahui bahwa seluruh senyawa benzoquinoline memiliki nilai fit-skor di
atas 50%. Hal ini menunjukan bahwa senyawa turunan benzoquinoline memiliki kemiripan interaksi
dengan ligan yang saat ini aktivitasnya dinyatakan sebagai senyawa aktif.
15. ABSORPTION PREDICTION

The second step in our test is to calculate ADME predictions. The absorption prediction calculated the
value of human intestinal absorption (HIA). Human intestinal absorption indicates the value of drug
 absorption by the human intestine. Based on the table, the compounds that were eliminated were
compounds b1, b3, b5, b7, b10 and b14. The compound "has an HIA value of less than 70-100%, so it will
affect the bioavability of the compound in the blood.

Tahapan kedua dalam pengujian kami adalah mengkalkulasi prediksi ADME. Pada prediksi absorbsi
dihitung nilai dari human intestinal absorption (HIA). Human intestinal absorption menunjukkan nilai
penyerapan obat oleh usus manusia. Berdasarkan tabel, senyawa yg dieliminasi ialah senyawa b1, b3, b5,
b7, b10 dan b14. Senyawa” tersebut memiliki nilai HIA yg kurang dari 70-100% sehingga akan
mempengaruhi bioavabilitas senyawa tsbt didlm darah.
16. DISTRIBUTION PREDICTION

Furthermore, the second parameter is distribution prediction, in the distribution prediction the blood-brain
barrier (bbb) penetration is calculated, which means that bbb can show the properties of the compound in
crossing the blood-brain barrier. Blood brain barrier needs to be avoided so as not to have an effect on the
central nervous system. Reference value of bbb is <1.00. Anti-covid drugs are not designed to cross the
brain barrier, so based on the following table, b2 compounds are eliminated because they can cross the
blood brain barrier

Selanjutnya parameter kedua adalah prediksi distribusi, pada prediksi dstribusi dihitung penetrasi blood-
 brain barrier (bbb), yg dmn bbb dpt menunjukkan sifat senyawa dlm melewati sawar darah otak. Sawar
darah otak perlu dihindari agar tidak menimbulkan efek pada sistem saraf pusat. Nilai rujukkan dari bbb
adlh < 1.00. Obat anti covid tdk didesign melewati sawar otak, sehingga berdasarkan tabel berikut,
senyawa b2 dieliminasi karena dapat menembus sawar darah otak
17. THE PREDICTION OF METABOLISM AND TOXICITY

The last parameter is prediction of metabolism & toxicity. In metabolic predictions, drug interactions with
hlm (human liver microsomal) & cytochrome P450 (CYP) inhibitors were seen. HLM is a parameter to
exclude drugs that are metabolized too quickly by the liver, whereas CYP is an enzyme that inhibits drug
metabolism so that it will reduce the therapeutic effect of the drug. Based on the table, the compounds that
were eliminated were compounds B3, B4, B5, B6 and B12

Then, in the prediction of toxicity, the ability of the compound to cause hepatotoxic & cardiotoxicity was
assessed. Based on the table, benzoquinolin (b1-b14) derivatives, do not have hepatotoxic & cardiotoxic
properties. This proves that all benzo derivatives have a much better performance than the parent
compound, benzoquinolin and also current drug therapy regimens, namely remdesivir & ritonavir.

Parameter terakhir ialah prediksi metabolisme & toksisitas. Pada prediksi metabolisme dilihat interaksi
obat dgn hlm (human liver microsomal) & sitokrom P450 (CYP) inhibitor. HLM merupakan parameter
 untuk mengeksklusi obat yang terlalu cepat dimetabolisme oleh hati, sedangkan CYP merupakan enzim
penghambat metabolisme obat sehingga akan mengurangi efek terapeutik obat. Berdasarkan tabel,
senyawa yg dieliminasi ialah senyawa B3, B4, B5, B6 dan B12

Kemudian, pada prediksi toksisitas, dilihat kemampuan senyawa u/ menyebabkan hepatotoksik &
kardiotoksik. Berdasarkan tabel, senyawa turunan benzoquinolin (b1-b14), tidak memiliki sifat
hepatotoksik & kardiotoksik. Hal ini membuktikan bahwa seluruh turunan senyawa benzo memiliki
performa yg jauh lebih baik dibandingkan dgn senyawa induknya, benzoquinolin dan juga regimen terapi
obat pd saat ini, yaitu remdesivir & ritonavir
18. MOLECULAR DOCKING SIMULATION
19.
20. LIPINSKI’S RULE OF FIVE FILTER
21.
The fourth and final stage is Lipinski's Rule of Five filter. Lipinski's Rule of Five is a rule that reads
(READ). In Rule of Five there is tolerance for as much as one violation. In this fourth stage filter, we
focus on the two potential compounds based on the results of the previous stages, namely compounds B9
and B14. Compound B9 has 1 violation of the Rule of Five so it meets the rules and can be administered
orally, while compound B14 has 2 violations of the Rule of Five so compound B14 is not suitable for oral
 administration. To find a suitable route of administration for compound B14, further analysis is required.

Tahap yang keempat sekaligus terakhir adalah filter Lipinski’s Rule of Five. Lipinski’s Rule of Five
merupakan aturan yang berbunyi (BACA). Pada Rule of Five terdapat toleransi sebanyak satu
pelanggaran. Pada filter tahap keempat ini kami berfokus pada kedua senyawa yang berpotensi
berdasarkan hasil tahapan - tahapan sebelumnya yaitu senyawa B9 dan B14. Senyawa B9 memiliki 1
pelanggaran Rule of Five sehingga memenuhi aturan dan mampu diadministrasikan secara per oral,
sedangkan senyawa B14 memiliki 2 pelanggaran Rule of Five sehingga senyawa B14 tidak cocok untuk
diadministrasikan secara oral. Untuk menemukan rute administrasi yang cocok untuk senyawa B14,
diperlukan analisis yang lebih lanjut.
22. SCIENTIFIC CONCLUSION

23. FUTURE AND CHALLENGES