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INVESTIGATION INTO CELL SURFACE RECEPTOR INHIBITORS FROM

Lignosus rhinocerus TM02® AS POTENTIAL PHARMACOLOGICAL AGENTS
FOR RESPIRATORY HEALTH

Goh Neng Yao1, Fung Shin Yee*1, Muhammad Fazril Mohamad Razif*1,
Ng Chyan Leong2 & Yeannie Hui Yeng Yap3

Medicinal Mushroom Research Group (MMRG), Department of Molecular Medicine, Faculty of

1

Medicine, University of Malaya, Kuala Lumpur; 2Institute of Systems Biology (INBIOSIS), Universiti
Kebangsaan Malaysia, Bangi; 3Department of Oral Biology and Biomedical Sciences, MAHSA University,
Selangor, Malaysia

*Corresponding author: syfung@ummc.edu.my

Renin–angiotensin–aldosterone system (RAAS) consists of cell surface receptors of human angiotensin-

converting enzyme 2 (ACE2) and angiotensin-converting enzyme (ACE) and is important for the
homeostasis of both the cardiovascular and respiratory systems. ACE2 is involved in the mechanism of
infections for SARS-associated coronavirus while ACE partakes in angiotensin II generation and
bradykinin degradation that leads to conditions such as inflammation and acute lung injury. Thus, inhibition
of ACE/ACE2 receptors are a promising way to prevent infection and mitigate its associated inflammatory
conditions. Lignosus rhinocerus TM02® (Tiger Milk mushroom) is traditionally used to alleviate
respiratory condition such as cough and asthma, supported by numerous scientific studies on its anti-
inflammatory properties. Past genomic-transcriptomic analysis of L. rhinocerus TM02® revealed the
presence of potential ACE inhibitory proteins in mushrooms, similar to Ganoderma lucidum. This study
serves to identify potential ACE/ACE2 inhibitors derived from L. rhinocerus TM02® via in silico molecular
docking studies and in vitro kinetic investigations. The identification and validation of bioactive proteins
from nature and their activities will provide a new avenue for the development of natural compounds for
pharmaceutical prevention of diseases and health maintenance.

Keywords: Tiger milk mushroom, ACE inhibitor, ACE2 inhibitor, molecular docking, protein modelling
 MARTINI COARSE-GRAIN MD SIMULATION ENABLES SELECTION OF BEST
DOCKING POSE FOR DEEP MUTATIONAL SCANNING TO GENERATE DISTINCT
MUTANT ANTIBODIES AGAINST CXCR2

Alif Nordin1,3, Shahrul Bariyah Binti Sahul Hamid2, Mohammad Tasyriq Bin Che Omar*1

School of Distance Education, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
1
2
Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam 13200 Kepala Batas, Pulau Pinang
Malaysia
3
Pusat Jaminan Kualiti, Universiti Islam Antarabangsa Sultan Abdul Halim Mu'adzam Shah
09300 Kuala Ketil Kedah Darul Aman, Malaysia

*Corresponding author: mtasyriq@usm.my

XXX

Keywords: Tiger milk mushroom, ACE inhibitor, ACE2 inhibitor, molecular docking, protein
modelling
Original Text
Word count: 220

1. The dynamics of antibody-antigen interactions is highly dependent on the 3D structure

of the antibody-antigen complex, which can only be achieved by computational protein-
protein docking.
2. Correct prediction of antibody-antigen model docking is the most integral component in
imparting further optimizations on the antibody towards antigen using computational
tools.
3. Incorrect prediction can lead to less or no appreciable improvement of antibody-antigen
binding.
4. Coarse-grain MD (CGMD) simulation can achieve at least an order of magnitude
increase in speed for simulation time compared to atomistic MD simulation with lesser
requirements for hardwares.
5. An optimised determination of antibody-antigen complex docking plus the prowess of
CGMD simulation paved an easy & reliable method to predict the correct docking poses
and allow further improvement on specificity and affinity of the antibody.
6. Here, we reported an easy & reliable method to select the best docking pose and deep
mutational scanning to generate distinct mutant antibodies against human CXCR2
receptor.
7. 5% ClusPro rule and heated CGMD simulation shortlisted two complex poses from 30
complex poses generated from ClusPro docking server.
8. Trajectories from long simulation was performed onto the two complex poses to get the
interaction dynamics of antibody residues against CXCR2.
9. The residues were shortlisted and submitted for deep mutational scanning.
10. AbLIFT webserver produced 50 possible mutant antibodies each with distinct interaction
profile.
Draft 1
Word count: 220229

1. The dynamics of antibody-antigen interactions is highly dependent on the 3D structure

of the antibody-antigen complex, which can only be achieved by computational protein-
protein docking.
2. Correct prediction of antibody-antigen model docking is the most integral component in
imparting further optimizations on the antibody towards antigen using computational
tools.
3. Incorrect prediction can lead to less or no appreciable improvement of antibody-antigen
binding.
4. Coarse-grain MD (CGMD) simulation can achieve at least an order of magnitude
increase in speed for simulation time speed compared to atomistic MD simulation with
lesser requirements for hardwareshardware.
5. An optimised determination of antibody-antigen complex docking plus the prowess of
CGMD simulation paved an easy & reliable method to predict the correct docking poses
and allow further improvement on specificity and affinity of the antibody.
6. Here, we reported an easy & reliable method to select the best docking pose and deep
mutational scanning to generate distinct mutant antibodies against human CXCR2
receptor.
7. 5% ClusPro rule and heated CGMD simulation shortlisted two complex poses from 30
complex poses generated from ClusPro docking server.
8. Trajectories from long simulation was performed onto the two complex poses to get the
interaction dynamics of antibody residues against CXCR2 and analysed using TTClust
software.
9. The residues were shortlisted using PyContact software and submitted for deep
mutational scanning.
10. AbLIFT webserver produced 50 possible mutant antibodies each with distinct interaction
profile.